Edward Jay Epstein, an author whose deeply researched books challenged conventional wisdom about controversies ranging from whether John F. Kennedy was killed by a lone assassin to whether the whistle-blower Edward Snowden was really a Russian spy, died Jan. 9 in Manhattan. He was 88.

A professional skeptic, Mr. Epstein wrote more than two dozen nonfiction books, many involving allegations of government conspiracies and corporate dereliction.

He earned his doctorate in 1972 from the Harvard-M.I.T. Joint Center for Urban Studies, taught political science at Harvard, the University of California/Los Angeles, and M.I.T., and he wrote for The New Yorker. But he returned to New York in order to become a full time author rather than pursue an academic career. “I wanted to be in New York, ever since I met Clay Felker,” the editor of New York Magazine, he said in an interview last year with the online magazine Air Mail. “He knew the world.”