Hey there- Sorry to say, but moorage in the Tokyo area is very expensive. Here is a good directory of marinas
Look into Chiba and surrounding areas. I once looked into moorage in Yokohama and they wanted something like 1100USD per month plus a 20% deposit on the yearly rate. Maybe you could look into somewhere outside the city and use the money
you'd save on train fare. The Shinkansen will get you there in no time. I have seen moorage here in Hiroshima for about 300usd/month for a 30ft mono. Let me know if I can offer any more assistance! Sail-Japan is a great resource.. Also keep in mind that you need a license
to operate anything with a motor
here and they don't accept foreign accreditation. The test is offered in English
though and isn't difficult.