Hi Sarah,
When I was diagnosed as an infant, I went to Oakland Children's Hospital. We didn't like the facility, but my family and I LOVED my pediatrician. Luckily, she soon became affiliated with UCSF, which was a wonderful improvement. The only problem for you is that her office is in Walnut Creek, not San Francisco. It's more like a satellite clinic that still sends its patients to UCSF. But, since all I have is personal experience, I cannot recommend her more highly. Her name is Nancy Lewis. Her colleagues are wonderful, as well, but she was always my primary pulmonologist. I drove the 2.5 hours each direction every two or three months just to see her. I was always pleased with the pediatric program at UCSF (the actual hospital, I mean), as well.
Now that I've transferred to the adult clinic at UCSF, I'm not as happy. I'm seriously considering transferring to Stanford, as I've only ever heard wonderful things about it. I have certainly been frustrated by the breakdown of communication at UCSF at times, but I imagine those problems arise at any big hospital.
Good luck with your choice! Feel free to contact me directly if you would like any more information about UCSF. I have about 12 years of experience there.