Gay hotels in the narrower sense are rare in Tokyo, but the city as a whole is relaxed in dealing with queer travelers. If you want to live close to the scene, it's best to look in Shinjuku, because the Ni-chome district with its bars is within walking distance from there. There are accommodations in all price ranges around Shinjuku Station, from simple business hotels to larger houses with views over the city. The location is also convenient because Shinjuku is one of Tokyo's largest transport hubs and you can quickly get to other parts of the city from here.
But you're not fixed on Shinjuku. Neighborhoods like Shibuya or Shinagawa are well connected and just as uncomplicated, when two men book a double room. In Japan, this is not an issue. At the reception, people rarely ask. Those who plan sightseeing rather than long nights are often quieter elsewhere and can take the metro or JR lines to Ni-chome in a few minutes. If your visit falls during Tokyo Pride at the beginning of June, you should plan earlier, because then central houses are quickly booked up and more expensive. The following selection will help you match location and house for your stay.