SF National Maritime Museum @ Hyde St Pier near Pier 43 ferry stop, Oakland Museum of California near Lake Merritt Bart, USS Hornet Museum in Alameda, Ride the Ferry just to ride the ferry and it is much easier than trying to drive across the bay, use the Bart to get around and just wander around the Embarkadero, and Market street Bart stations.
There are lots of museums but I would save some of those for when the wife gets back. I particularly liked the Legion of Honor and most of the De Young. Use this link
Wiki link to museums and take your pick. You might like the Cartoon Museum. :C
I enjoyed just wandering around and riding the bus but what ever your taste, there is a place in SF of interest.
