Yes - in addition to Alameda, there was the sub base at Mare Island, Hunter's Point ship yard, the Concord Naval Weapon's station, Oak Knoll Naval Hospital, and Treasure Island Naval Station. And not just Navy - the Coast Guard station on Yerba Buena Island, the Presidio (Army), the Army base (I forget it's name) on the north side of the Golden Gate Bridge, mostly housing, but they also had Nike missile batteries there, the Oakland Army Depot, and the Army Air Field in Navato.
Don't forget Treasure Island. Was out there for classes a couple times and rented boats for excursions on the Bay.