If you haven't been, Shinjuku ni-chome is the traditional gay location in Tokyo. I recall getting accosted on the street there by a young Japanese guy who was totally into my western Salary Man vibe. The fact that he felt coming at me on the street was sort of wonderful. Alas, I had other interests at the time. To me, at least, Shinjuku ni-chome is a bit of a pilgrimage site, the heart of old tokyo gay life.
But, I've not used any of the agencies yet, so can offer no comment on them.