If you search for "gay bar" on Google Maps in Tokyo, you will find over a hundred places. Many of those are really small, sometimes they only a capacity of just 10 people.
These small bars vary from cocktail bar, to "underwear only lounges". Sometimes the name gives it away, sometimes it's more a surprise what to expect.
Many of these small bars are located on the 2nd, 3rd or even up to the 5th floor of buildings. So from the outside you will not have any idea what to expect. You have to be a little adventurous to find out!
Not all bars (and restaurants) are welcoming foreign people. Don't be offended by this. If we understand well it's mainly because many Japanese are still not used to foreigners and like to stick with their own traditions and customs.
You find soon enough if a place is foreigner friendly. If not they will just say something the place is full. Even when the place is obviously empty.
Gay bars to start
Shinjuku also features some large ground floor places that are easy to find, with no surprises. The Tokyo Eagle is a good place for drinks to start the evening. Later on the more club style Tokyo Eagle Blue is located in a relative large basement around the corner. Both places attract a lot of expats and tourists.