Try the Castle Inn. No frills, but safe and secure and good value. 
15 min walk to the Wharf, 25 to Union Sqaure (shopping). 10 minute bus from Union Square ride drops you off in front of the hotel. 
 
Extremely friendly owners...a good deal when we went last year. Free parking (although that doesn't seem an issue) which is cheaper then the $20 per night. 
 
Bart from the Wharf, or downtown (or even, with the correct bus schedules, from the hotel) will take you to SBC/ATT (took a tour there last time, nice facilities) Park. 
 
Avoid Oakland at most costs..besides relativiley nothing to do tourist wise, it is the skectichest place I've ever been when the sun goes down...and we were in the outskirts of town in a seemingly respectable area.
		 
		
		
		
		
		
		
		
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