I highly recommend George Chauncey's Gay New York on this. I'm going to base this answer on his article in The Encyclopedia of LGBT History in America edited by Marc Stein (Scribner's, 2004), which I worked on.

Chauncey makes a strong argument for gay visibility, and there were definite gay subcultures from Walt Whitman's time on. The Bowery was one locus; there were dance halls with "female impersonator" dance partners; there was, of course, Greenwich Village. In the 50s, you would have known where the "fairies" were reputed to hang out; the bars such as the "Bird Circuit" on Third Avenue; the drag shows at Webster Hall. After World War II, new gay communities formed in Brooklyn Heights, Jackson Heights, and the East Side of Manhattan. And there was always Broadway and other performing and visual arts, which have always had a huge gay presence. A New York chapter of the Mattachine Society formed in 1955, and the Daughters of Bilitis in 1958.

Finally, there were known cruising spots, such as parks, bathhouses, and, of course, public bathrooms ("t-rooms").