I don't think there is any question about which gay-centric film was first. Others may have included minor gay characters, but none explored more comprehensively the sexual politics of gay men than the revolutionary
The Boys in the Band
The film, from 1970, debuted two years after the off-Broadway production by the same name and roughly one year after the famous Stonewall incident that you refer to in the title of the thread.
It isn't easy to watch today because of the perception that the characters are cliches or that they represented a repressed and self-loathing period of time before gays became empowered.
Director William Friedkin, who also directed such classics as the Exorcist and The French Connection, has remarked that he "knew that gay characters had not been portrayed on film in any significant way at all, so I knew this would push the envelope in a lot of places around the country and to a lot of people. I was most surprised that most of the negative attitudes about it came from organized gay groups. All that's changed over the years. You look at [online] postings about it now and the reviews are fantastic. They view it as the way gay life was at the time and is no longer. A lot of critics felt it was trying to keep gay people in a kind of ghetto, in the closet, but now look back and see that it really opened doors to gay characters on TV and in all walks of life as people in the culture. "
Yeah, actually I'd say that suggesting the film Cruising is right on topic.
It might not have been the most flattering depiction of gay life in the early 1980s, but it certainly was groundbreaking. To have a marquee star like Al Pacino work on a film about anonymous gay sex certainly was a watershed in LGBT film.