We've got amphibious assault assets in Sasebo (Kyushu) and White Beach (Okinawa) but it's true that the bulk of 7th Fleet's major surface combatants are based out of Yokosuka (Yokohama).

I don't know if they had any basing rights at the time I was there, but given the USG was delivering weapons (military ships, etc) there was a large presence there at that point in time. I only know that through actual observations while on bases there.