It would be difficult to rent a room with studio in urban area in Japan.
Instead, you can rent rehearsal studio. I usually use "Studio Penta" in Shinjuku.
http://www.studiopenta.net/rehearsal/shinjuku.html
Studio Penta Otsuka (20 minutes from Shinjuku by train) is much cheaper than Shinjuku.
http://www.studiopenta.net/rehearsal/ohtsuka.html