The real choice is either Oakland (if not during commute hours) or Sacramento. Sac is a little farther awary, however its a much smaller airport with easier in and out and a lot less traffic. If its during commute hours sac is by far easier for coming and going.
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It's usually much less expensive to choose Oakland It really depends on the airlines and the destination though but over the years I have rarely found SFO to be the low price.
The cheapest from SFO is $207 round trip on Delta, Alaska or United.The cheapest from OAK is $246 round trip on Southwest, or $298 on Alaska as the cheapest “full service” airline. SFO has more competition between airlines, and OAK is more convenient for many people who live in the Bay Area.
There are 3 international airports in San Francisco - San Francisco International Airport (SFO/KSFO), Norman Y. Mineta San José International Airport (KSJC), and Oakland International Airport (KOAK).