In the 1947 Everson case, the Supreme Court essentially nationalized Madison and Jefferson's "Virginia Plan" on disestablishment. Subsequent scholarship has aptly noted, while the Founders generally agreed on religious liberty, they disagreed on establishment policy. Therefore, religion (especially establishment policy) was left to the states. Virginia was the most "disestablished" state. Massachusetts was the most "established" state. Most of the other states were somewhere in between. They tend to be ignored or at least less focused on.
Jefferson and Madison, of course, formulated the policy that prevailed in Virginia. John Adams to an extent, represents the Massachusetts' view. Adams helped write Mass.'s original constitution which contains its view on religion and government.
William Livingston, originally from New York, wrote on church-state issues, as a New Yorker, in the Independent Reflector magazine. Later, as governor of New Jersey, Livingston wrote, under the pseudonym "Cato," two addresses on church-state policy that referenced provisions New Jersey's state constitution. The addresses were published in 1788 in the American Museum magazine.
Here is the relevant provision of NJ's Constitution:
XVIII. That no person shall ever, within this Colony, be deprived of the inestimable privilege of worshipping Almighty God in a manner, agreeable to the dictates of his own conscience; nor, under any presence whatever, be compelled to attend any place of worship, contrary to his own faith and judgment; nor shall any person, within this Colony, ever be obliged to pay tithes, taxes, or any other rates, for the purpose of building or repairing any other church or churches, place or places of worship, or for the maintenance of any minister or ministry, contrary to what he believes to be right, or has deliberately or voluntarily engaged himself to perform.
XIX. That there shall be no establishment of any one religious sect in this Province, in preference to another; and that no Protestant inhabitant of this Colony shall be denied the enjoyment of any civil right, merely on account of his religious principles; but that all persons, professing a belief in the faith of any Protestant sect. who shall demean themselves peaceably under the government, as hereby established, shall be capable of being elected into any office of profit or trust, or being a member of either branch of the Legislature, and shall fully and freely enjoy every privilege and immunity, enjoyed by others their fellow subjects.
It's not as established as Mass., nor as disestablished (or religiously equal) as Virginia. Yet the rhetoric that Livingston uses to defend New Jersey's model is arguably more anti-clerical, anti-establishment, pro-religious liberty than Jefferson's and Madison's Virginia's documents.
Also notable is Livingston's Lockeanism. Although Jefferson and Madison's documents likewise build from a Lockean there is far more explication of Lockean theory in Livingston's two Cato addresses.
I've already uploaded the two "Cato" documents but it seems I am going to have to write out some of its passages before I get more folks to reflect on the ideas.
I just found on googlebooks, the February 18, 1778 address by Livingston, which I can copy, paste and reproduce.
"If, in our estimate of things, we ought to be regulated by their importance, doubtless every encroachment upon religion, of all things the most important, ought to be considered as the greatest imposition; and the unmolested exercise of it, a proportionable blessing.
By religion, I mean an inward habitual reverence for, and devotedness to the Deity, with such external homage, either public or private, as the worshipper believes most acceptable to him. According to this definition, it is impossible for human laws to regulate religion without destroying it; for they cannot compel inward religious reverence, that being altogether mental and of a spiritual nature; nor can they enforce outward religious homage, because all such homage is either a man's own choice, and then it is not compelled, or it is repugnant to it, and then it cannot be religious.
The laws of England, indeed, do not peremptorily inhibit a man from worshipping God, according to the dictates of his own conscience, nor positively constrain him to violate it, by conforming to the religion of the state: But they punish him for doing the former, or what amounts to the same thing, for omitting the latter, and consequently punish him for his religion. For what are the civil disqualifications and the privation of certain privileges he thereby incurs, but so many punishments? And what else is the punishment for not embracing the religion of others, but a punishment for practising one's own? With how little propriety a nation can boast of its freedom under such restraints on religious liberty, requires no great sagacity to determine. They affect, tis true, to abhor the imputation of intolerance, and applaud themselves for their pretended toleration and lenity. As contra-distinguished, indeed, from actual prohibition, a permission may doubtless be called a toleration; for as a man is permitted to enjoy his religion under whatever penalties or forfeitures, he is certainly tolerated to enjoy it. But as far as he pays for such enjoyment, by suffering those penalties and forfeitures, he as certainly does not enjoy it freely. On the contrary, he is persecuted in the proportion that bis privilege is so regulated and qualified. I call it persecution, because it is harassing mankind for their principles; and I deny that such punishments derive any sanction from law, because the consciences of men are not the object of human legislation. And to trace this stupendous insult on the dignity of reason to any other source than the one from which I deduced it in the preceding essay, I mean the abominable combination of King-Craft and Priest-Craft, (in everlasting indissoluble league to extirpate liberty, and erect on its ruins boundless and universal despotism,) would I believe puzzle the most assiduous enquirer. For what business, in the name of common sense, has the magistrate (distinctly and singly appointed for our political and temporal happiness) with our religion, which is to secure our happiness spiritual and eternal? And indeed among all the absurdities chargeable upon human nature, it never yet entered into the thoughts of any one to confer such authority upon another. The institution of civil society I have pointed out as originating from the unbridled rapaciousness of individuals, and as a necessary curb to prevent that violence and other inconveniences to which men in a state of nature were exposed. But whoever fancied it a violence offered to himself, that another should enjoy his own opinion? Or who, in a state of nature, ever deemed it an inconvenience that every man should choose his own religion? Did the free denizens of the world, before the monstrous birth of Priest-Craft, aiding by and aided by the secular arm, ever worry one another for not practising ridiculous rites, or for disbelieving things incredible? Did men in their aboriginal condition ever suffer persecution for conscience sake? The most frantic enthusiast will not pretend it. Why then should the members of society be supposed, on their entering into it, to have bad in contemplation the reforming an abuse which never existed? Or why are they pretended to have invested the magistrate with authority to sway and direct their religious sentiment? In reality, such delegation of power, had it ever been made, would be a mere nullity, and the compact by which it was ceded, altogether nugatory, the rights of conscience being immutably personal and absolutely inalienable, nor can the slate or community as such have any concern in the matter. For in what manner doth it affect society, which is evidently and solely instituted to prevent personal assault, the violation of property and the defamation of character; and hath not (these remaining inviolate) any interest in the actions of men—how doth it, I say, affect society what principles we entertain in our own minds, or in what outward form, we think it best to pay our adoration to God? But to set the absurdity of the magistrate's authority to interfere in matters of religion, in the strongest light, I would fain know what religion it is that he has authority to establish? Has he a right to establish only the true religion, or is any religion true because he does not establish it? If the former, his trouble is as vain as it is arrogant, because the true religion being not of this world, wants not the princes of this world to support it, but has in fact either languished or been adulterated wherever they meddled with it. If the supreme magistrate, as such, has authority to establish any religion he thinks to be true, and the religion so established is therefore right and ought to be embraced, it follows, since all supreme magistrates have the same authority, that all established religions are equally right, and ought to be embraced. The emperor of China, therefore, having, as supreme magistrate in his empire, the same right to establish the precepts of Confucius, and the Sultan in his, the imposture of Mahomet, as hath the king of Great Britain the doctrine of Christ in his dominion, it results from these principles, that the religions of Confucius and Mahomet are equally true with the doctrine of our blessed Saviour and his Apostles, and equally obligatory upon the respective subjects of China and Turkey, as Christianity is on those within the British realm; a position which, 1 presume, the most zealous advocate for ecclesiastical domination would think it blasphemy to avow.
The English ecclesiastical government, therefore, is, and all the religious establishments of the world, are manifest violations of the right of private judgment in matters of religion. They are impudent outrages on common sense, in arrogating a power of controlling the devotional operations of the mind and external acts of divine homage not cognizable by any human tribunal, and for which we are accountable only to the Great Searcher of hearts, whose prerogative it is to judge them.
In contrast with this spiritual tyranny, how beautiful appears our catholic constitution in disclaiming all jurisdiction ever the souls of men, and securing, by a law never to be repealed, the voluntary, unchecked moral suasion of every individual, 'and his own self directed intercourse with the father of spirits, either by devout retirement or public worship of his own election. How amiable the plan of entrenching, with the sanction of an ordinance, immutable and irrevocable, the sacred rights of conscience, and renouncing all discrimination between men on account of their sentiments about the various modes of church government, or the different articles of their faith."
That's all the 1822 googlebooks reproduces. It is most, but not all, of Livingston's 1778 address. (For more, again, see here.)