I would say staying in Pacifica or HMB would be great. Its on the coast, and you get amazing views.
If you wanted a small town feel, and are near BART, I would HIGHLY reccommend staying in Walnut Creek or Laffayette. Walnut Creek is a great home base, imho, because it has great shops and restaurants. And you will be near BART, which is handy of course. I am from Walnut Creek, but whenever we have guests I usually point them in the direction of the
Embassy Suites Walnut Creek.
http://www.embassysuites.com/en/es/hotels/index.jhtml?ctyhocn=SFOPHES [nofollow] You are VERY close to BART, but don't worry, it wont bother you in your room.
If you do happen to stay in WC, let me know and I can point in the right directions for what you are looking for. For example, from WC, it only takes a little less than an hour until you are in Napa, or if you need good food recs...
You are going to have a fantabulous time, I am sure...