Most of them were deists. Thomas Paine, Ben Franklin and Thomas Jefferson were all deists (although there is speculation, and good speculation, that Jefferson was more of a Unitarian than a deist, or something not all together easily categorized back then).

Ben Franklin on deism:

My Parents had early given me religious Impressions, and brought me through my Childhood piously in the Dissenting Way. But I was scarce 15 when, after doubting by turns of several Points as I found them disputed in the different Books I read, I began to doubt of Revelation itself. Some Books against Deism fell into my Hands; they were said to be the Substance of Sermons preached at Boyle's Lectures. It happened that they wrought an Effect on me quite contrary to what was intended by them: For the Arguments of the Deists which were quoted to be refuted, appeared to me much Stronger than the Refutations. In short I soon became a thorough Deist.

Thomas Paine was afraid of running "headlong into atheism" in a letter to Sam Adams, and admitted to believing in God. His Age of Reason proves that he was not a particularly devout creationist of any sort, and scolded most forms of organized religion. Most autobiographies (I meant biographies, I am dumb) peg him as a deist. He also wrote this:

The opinions I have advanced ... are the effect of the most clear and long-established conviction that the Bible and the Testament are impositions upon the world, that the fall of man, the account of Jesus Christ being the Son of God, and of his dying to appease the wrath of God, and of salvation, by that strange means, are all fabulous inventions, dishonorable to the wisdom and power of the Almighty; that the only true religion is Deism, by which I then meant, and mean now, the belief of one God, and an imitation of his moral character, or the practice of what are called moral virtues – and that it was upon this only (so far as religion is concerned) that I rested all my hopes of happiness hereafter.

Thomas Jefferson was a deist, although there are many good sources for him actually being a Unitarian. The wiki is as good a source as any on this. He rejected the trinity, wrote the infamous Jefferson Bible and said this:

"I am a Christian, in the only sense in which Jesus wanted anyone to be: sincerely attached to his doctrines, in preference to all others; ascribing to himself every human excellence; and believing he never claimed any other."

John Adams was also a Unitarian, I believe, and was a member of First Parish Church in Quincy according to letters between him and his son, John Quincy.

"I acknowledge myself a unitarian -- Believing that the Father alone, is the supreme God, and that Jesus Christ derived his Being, and all his powers and honors from the Father."

Alexander Hamilton grew up fairly evangelical, and was definitely some sort of Christian, although I don't believe he ever professed to being a deist. He makes several mentions of God, and according to Gordon Wood in Empire of Liberty he was "a conventional liberal with theistic inclinations who was an irregular churchgoer at best."

Suffice it to say that most of the Founding Fathers, or the really famous ones, were deists, Unitarians or some other kind of Christians. The only notable examples I can think to this are Ethan Allen, who had a lot of conflicting things to say about religion, and wrote in his Reason: The Only Oracle Of Man: A Compendious System Of Natural Religion:

"as to being a Deist, I know not, strictly speaking, whether I am one or not, for I have never read their writings"

The other is Aaron Burr, who would probably not be described as a Founding Father, but a contemporary of them nonetheless. On his deathbed he was asked to profess that God is real by Reverend P.J. Van Pelt, and he said:

"On that subject I am coy."