Was Thomas Paine a Democratic-Republican, Federalist, or an independent?
His views were most closely associated with the Anti-Federalists. There were, of course, no party registrations in those days.
I’d call Paine an independent iconoclast who didn’t get along with any form of organized authority.
His closest alliance with any party was with the Girondists during his time in the French National Assembly.
The idea of political parties in the nascent nation was anathema to many of the Founders.
In fact, George Washington famously warned against the ‘baneful effects’ of political parties.
And Paine made himself persona non grata with many Americans when he directly attacked the President in Washington’s second term. See the last two paragraphs here:
Given that Paine left the U.S. to live in Britain in 1787, the year the Constitution was written, later moving to France until 1802, it is unlikely that he was much involved with political parties of any stripe. However, it would probably not be wrong to characterize him as an Anti-Federalist or, possibly, Democratic-Republican leaning for the last six years of his life, based on his opposition by the Federalists and his friendship with Jefferson.
He was definitely far more sympathetic to the Democratic-Republicans than the Federalists, the latter were suspiscious of people like Paine because of his sympathy for the French Revolution, anti-Britishness, and general radicalism.