They thought they were (except for Ethan Allan and Thomas Paine who said they were not Christians). The confusion arises because Unitarians do not believe in the Nicene Creed. They are heretics but they are Christian heretics who trace their cause to Arian in the 4th century A.D.
Jefferson annotated the New Testament because he saw Christ as the perfect teacher (Unitarians tend toward Judaism in that respect. Jesus was a reforming rabbi). Thomas was purifying Christianity just as he, and others, were purifying politics--stripping it of blind obedience and a ruling class.
Today most Unitarians are not Christian of course. But they were in Jefferson's day. Those who were more liberal and did not view Christ as the center of their beliefs belonged to the Universalist church . The headquarters of both were only a few blocks apart in Boston. Don't believe any of the founders were Universalists.
Curiously enough, one year after Jefferson expressed his wish that all Americans would become Unitarians, there was a fierce battle in Massachusetts between Universalists and Unitarians. The latter were supported by state taxes. The Universalists wanted to change the state constitution and prohibit that practice. Daniel Webster, a Unitarian himself, argued the church served a useful function and deserved state support. He won. But not for long. By the mid 1830s, state financing of churches was ended in the state.