William Whipple 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: 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 142-143:
William Whipple, a sea captain turned merchant, retired from business to further the Revolution. IN addition to sitting in Congress, he commanded New Hampshire militia in two major campaigns and held various State offices. ...he passed away in 1785 at the age of 55 at Portsmouth, where he was buried in Union Cemetery.
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.