You might plan to attend mass at San Francisco de Asis (Mission Dolores) in San Francisco. This is the most authentic mission in the Bay area and the only original church.
The Mission Dolores chapel is quite small and thus they do not hold Mass on Sunday (it is held at the adjacent cathedral) but you could say a prayer in the mission itself while there....or attend the special Saturday night vigil mass (5:00 p.m.) at the chapel. Mass is also held at the old mission at 7:30 and 9:00 a.m. M-F.
Depending on where you are staying you can certainly find Mass services at the mission replica in Santa Cruz (a modern Victorian era church is on the original site of the mission) or Santa Clara (where there is a modernized version of the original church. The San Jose Church (north of the city of San Jose) was tastefully and carefully restored. If you are up for a drive the mission at San Juan Bautista is really charming and authentic. They also have a Saturday 5 p.m. vigil mass and three services Sunday morning.