Definitely check the API scores. There are two reports you want to look at: the most recent base scores report and the 2008 growth report for each county where you would consider living (that seems like a lot, but you can get through it in an hour). The state scores each district one to ten (ten being the highest) for how that district's test scores compare to the others in the state. The other, perhaps more telling rating is the "similar schools" rating. This rating (also one to ten) tells you how well this school does when compared to other schools with similar student populations. That number comes closest to telling you how much of the achievement is from the school, and how much is from parents/community (it's not perfect, but it will help you weed through the thousands of schools). Also know that those "similar schools" numbers can change a couple of points from year to year, so don't get too hung up on a seven versus a nine. I would be less than thrilled with a three, though.
As someone who grew up attending some of California's highest-scoring schools, and now a teacher, I would strongly encourage you to visit the school and evaluate its culture. High scores often mean high pressure, lots of money and the superficiality that can accompany it, and a lack of parents at home (due to the need for two incomes and long commutes). The bay area is a big place, and the upside of that is that there are lots of places with top schools. Finding the right environment for your child will take some legwork, and the best fit may be a star school in a less than fabulous district, a charter school, or magnet. That said, the highest scoring places in the east bay (and closest to the city) are Piedmont, Orinda, Moraga, Mission San Jose in Fremont, and Bollinger Canyon in San Ramon. In the north bay, Kentfield and Ross Valley have strong scores. On the peninsula, there's Palo Alto, Woodside, Portola Valley, Las Lomitas, and Hillsborough (and more further south, though those are all closer to Silicon Valley). I hope that helps.