they're both about the same distance...most local people take sjc, people from further out take sfo. sjc has a shuttle that takes you straight to the caltrain station. hope this helps.
one more thing. if you take the caltrain to the stanford/palo alto station...take stanford's free bus shuttle to get to campus. it's called the marguerite.
I have been to Stanford a few times to compete in track and each time our team flew to San Jose. I believe San Jose is a little faster and the traffic seemed to be a little less then when we drove from San Fransisco to Stanford. San Jose is usually cheaper to fly into than San Fransisco is.
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