Flynn became an early and avid supporter of Senator Joseph McCarthy. This was in part because Flynn (even in his early left-wing views) had always been firmly anticommunist and in part because McCarthy shared Flynn's dislike for the Washington/New York establishment.

In 1955, Flynn had a formal falling-out with the new generation of Cold War, conservatives when William F. Buckley, Jr., rejected one of his articles for the new National Review. This submission had attacked militarism as a "job-making boondoggle." Flynn retired from public life in 1960. During his last years (he died in 1964) some of his books were promoted and reprinted by the John Birch Society.

For many years Flynn made his home in Bayside, New York in a large compound overlooking Little Neck Bay, with a house and a separate building he used as a broadcasting studio. He was a neighbor and friend of Mrs. James J. Corbett, the widow of boxing champion "Gentleman Jim" Corbett.