We've stayed at the RI at Oyster Point twice and enjoyed it. Very quiet area, and nice hiking trail. Rooms come with kitchen, etc. Staff was very good. You can take the shuttle to CalTrain, from there to 4th ST. SFO.

We've also stayed at the full service Marriott in San Mateo - not much furth dwon the peninsula. You can walk from there (5 minutes) to the CalTrain station for the city. Large property - nicely down and again a very good staff. If you've got a car they do charge for parking, but you can park on the street behind the hotel for free (done it 3x with no problems).

Either of these is nice, albeit not in the city.

Bruce