From a historical standpoint:
Initially, the major IJN yards, Yokosuka, Kure, Sasebo and Maizuro. Later as the war progressed, bases were established at Aomori Bay, Kwajalein, Rabaul, Penang, Surabaya, Palau, Cebu and Truk. Truk was one of the largest for the Japs during the war...
The hunting is good there until late '43 if I remember...
[EDIT] Sorry tater, I thought he was looking to do some sub hunting in my first post so I edited... Hence your response...