I would (and did) sacrifice some individual freedom and stay either with a Japanese host family or at a normal Japanese student hall of residence. Or, and this might be the best choice, share an apartment with a few Japanese students. I`ve done all three in the 90`s and while there were frustrating moments it`s worthwhile and let`s you experience Japanese customs and culture first hand. Everything in a society like Japan is based on a web of relationships and learning to live in it, so might be a good investment in your future.