Alexander Hamilton was a Presbyterian and an Episcopalian. Alexander Hamilton's mother was a Huguenot.
He was identified as an Episcopalian by: the Library of Congress and A Worthy Company: Brief Lives of the Framers of the United States Constitution, written by M. E. Bradford. (Source: Ian Dorion, "Table of the Religious Affiliations of American Founders", 1997).
From: Robert G. Ferris (editor), Signers of the Constitution: Historic Places Commemorating the Signing of the Constitution, published by the United States Department of the Interior, National Park Service: Washington, D.C. (revised edition 1976), pages 172-175:
Hamilton was born about 1755, apparently on the island of Nevis, in the Leeward group, British West Indies. He was the illegitimate son of a common-law marriage between a poor itinerant Scotch merchant and an English-French Huguenot mother who was a planter's daughter. In 1765, after the father had moved his family elsewhere in the Leewards to St. Croix in the Danish (now United States) Virgin Islands, he deserted his wife and two sons.
The mother, who opened a small store to make ends meet, and a Presbyterian clergyman provided Alexander with a basic education, and somehow he learned to speak fluent French. When he was 12 to 14 years old, about the time of his mother's death, he became an apprentice clerk at Christiansted in a mercantile establishment, whose proprietor became one of his benefactors.
...when Jefferson and Aaron Burr tied in Presidential electoral votes in 1800, Hamilton threw valuable support to Jefferson. In 1804, when Burr sought the governorship of New York, Hamilton again managed to defeat him. That same year, Burr, taking offense at remarks he believed to have originated with Hamilton, challenged him to a duel, which took place at present Weehawken, N.J., on July 11. Mortally wounded, Hamilton died the next day. He was in his late forties at death. He was buried at Trinity Churchyard in New York City. [Trinity Church is one of the oldest and most famous Episcopalian churchs in New York.]
Note that numerous sources and authoritative references have been consulted in order to ascertain the religious affiliation of the American Founding Fathers. Note that the excerpts and references mentioned on this page are not the only references used in order to identify this person's religious affiliation.