John Hancock was a Congregationalist.
He was identified as a Congregationalist by The Congregationalist Library. (Source: Ian Dorion, "Table of the Religious Affiliations of American Founders", 1997).
From: B. J. Lossing, Signers of the Declaration of Independence, George F. Cooledge & Brother: New York (1848) [reprinted in Lives of the Signers of the Declaration of Independence, WallBuilder Press: Aledo, Texas (1995)], pages 22-23:
One of the most distinguished personages of the War of Independence, was John Hancock, who was born near the village of Quincy, in Massachusetts, in the year 1737. His fther and grandfather were both ministers of the gospel. His father is represented as a pious, industrious, and faithful pastor; a friend of the poo, and a patron of learning. He died while John was quite an infant, and left him to the care of a paternal uncle, who cherished him with great affection.From: Robert G. Ferris (editor), Signers of the Declaration: Historic Places Commemorating the Signing of the Declaration of Independence, published by the United States Department of the Interior, National Park Service: Washington, D.C. (revised edition 1975), pages 67-69:
Hancock, born in 1737 at Braintree (present Quincy), Mass., lost his father, a Congregationalist pastor, at the age of 7. He spent the next 6 years with his grandparents at Lexington before joining his guardian, Thomas Hancock... in Boston. After studying at Boston Latin School and graduating from Harvard College in 1754, John began working as a clerk in his uncle's business...