Sorry for the late reply, but I just remembered some scuttlebut from back when we were homeported in Sasebo.
First, its a great town to visit and it was a great homeport for me back in the day (late 1980's).
Anyway, its not a museum as far as I know but there is a park near the entrance to the (US) base. In that park you'll find a small green cinder block building. The scuttlebut I heard more than once was that the raid on Pearl Harbor was planned inside that building.
At the time I was there, I was skeptical. Submariners are great at making anything sound plausible
but I heard it from people I trusted.