I would advise you to consider Yoshida Institute in Takadanobaba (2 stops from Shinjuku). The school is the place where I have studied Japanese, so please do your research and ask me if you have any questions.
I have studied long term there, but I know many people that actually study for 3 months in an intensive course at Yoshida and I had always great feedbacks from them.
Naganuma is very good too, but is in Shibuya (10 minutes train ride from Shinjuku).
A good place to start to look for info about the Yoshida Institute is the Go! Go! Nihon website, which is in my signature.