Thomas Stone was an Episcopalian.
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), page 136:
Stone entered politics in 1773 as a member of the Charles County committee of correspondence. The next year, on behalf of the Proprietary Governor, he helped prosecute Joseph H. Harrison, a Maryland legislator who refused to pay the poll tax for the support of the Anglican clergy. This action, despite its legal ethicality, did not endear Stone to the patriots. His opponents, counsel fo the defnese, consisted of Thomas Jefferson, Samuel Chase, and William Paca--all three of whom later became his congressional colleagues...
In 1787 Stone's wife, whose health had been failing for more than a decade, passed away at the age of 34. The grief-stricken Stone abandoned his work, declined to attend the Constitutional Convention to which he had been elected, and decided to visit England. A fw months later, though only in his mid-forties, he died suddenly while awaiting a vessel at Alexandria. Three of his children survived him. Stone is buried in the family graveyard adjacent to Habre-de-Venture.
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.