For animae and manga related stuff, I would recommend Mandarake, which has many specialist branches for new and used stuff, all in the same building: Nakano Broadway, on the second and third floors.

To get there, take the Chuo line (orange) or the Chuo-Sobu line (yellow) from Shinjuku station westbound -- away from Tokyo station -- to Nakano station. That takes 4-6 minutes. Go out the NORTH exit of the station. You will see an enclosed-mall like thing called Sun Mall. Walk through it, the building at the far end is Broadway Nakano. The first floor is useless, go up to floors 2 and 3.

I am guessing that "Mandarake" is a Japanification of "Mandrake," as in "Mandrake the Magician," but I really don't know.