Have you been to the store Lumiere in Ni-Chome? You can spot it easily because it always has a huge poster of Badi magazine outside. They carry a lot of popular gay mangaka including Gengoroh Tagame, Jiraiya, Kazuhide Ichikawa, Takeshi Matsu, Kumada Poohsuke, etc. But for a wider selection including more specialty doujinshi check out Big Gym in Ueno or Ikebukuro. Here’s a page with information on their two locations, including directions from the JR station: http://www.biggym.co.jp/bg-online/shop-guide.html
Big Gym is the most comprehensive gay shop I’ve been to in Tokyo, and they also carry some MASSIVE products! :) You can also find a smaller selection of gay manga and doujinshi at shops like Taco Che in Nakano Broadway, and certain Mandarake locations. I haven’t been to Osaka so I don’t know about shops there, but I would recommend asking for advice at the gay community center in Osaka, Dista!