I know this is a relatively old thread, but since I went through the same decision process last summer, and others may search for this topic again, I figure it's worth replying.
I chose UCSF, even though Stanford is much closer to my home and work (Stanford is a 30-minute drive, versus about an hour for UCSF). I picked UCSF because my local neurologist strongly recommended it over Stanford, and because my own research indicated that UCSF seems to have a stronger reputation. One metric I used for comparison was to search PubMed to see who was doing research and publishing results on Multiple Sclerosis. UCSF dominates in this area.
That said, I have gone to Stanford for other medical care, and I've always been happy. So I don't think Stanford is bad, just not as strong for MS specifically.