If you're planning on touring SF, the best place to stay is IN the city. If you have a car, you can always leave it in the hotel garage and then use to to visit Wine Country or the Coast (Sonoma or San Mateo). I wouldn't recommend staying at any of the airports (bad location, nothing to see/do and too far away), and I'm referring to SFO, Oakland and San Jose.

If you stay in the East Bay (Berkeley area) you have to deal with taking BART (the subway) which is expensive, not necessarily near a hotel, and crowded. I have had friends stay at the Courtyard by Marriott in Larkspur (Marin County) where you can park your car and take either a bus (Golden Gate Transit) or the Larkspur Ferry to San Francisco.

Joli Wilson San Rafael, CA