I've not stayed at any of these cities recently, so I hope others who have will weigh in with some recommendations for you. It might help if you would tell us a little about your trip plans (purpose, what sights you're interested in seeing, adults, kids, etc.)
Actually, if you're wanting to stay at an RI (kitchen amenities), I did stay at the RI in San Mateo once, and while it's not close (as in walking distance) to any attractions, it wasn't too far of a drive at all into the city for sightseeing. I remember the property being very nice, and that the food offerings were delightful, but that was about 15 years ago. It's also located just about exactly equidistant to both cities, if you are wanting to spend time in both places.
Thanks for posting. Hope we hear more from folks.
I have stayed in SFO in several properties, primarily for business, so the locations were choosen based on proximity to work, but I enjoyed all of them. CA traffic being what it is, I generally take the hotel closest to where I need to go, unless I absolutely can not stand that property.
I have no recent experience with RI in area. We did stay at Marriott San Jose recently and found it to be quite nice. Located next to Convention Center right in downtown - walk to shops, restaurants, etc. LIght rail can get you to train sta or onto SFO. Also stayed at Marriott Union Sq - also very nice right in heart of the city. Recommend either one.