All of the airports but one that have been mentioned are pretty well fenced and gated. In fact, you may have to inquire about a code to gain after-hours access. OTOH KHAF is easily accessed from the harbor area, by anyone. A plus if you’re flying in for lunch, but a minus if you’re concerned about security.
When are you coming? Pre-Covid I would recommend against a rental car. Parking in the Marina area was hard to find and/or expensive. Lots of traffic. Parking at suburban BART lots filled up by 7 am weekdays. However, currently, I believe that is not the case. BTW, a face mask is currently mandatory on all public transportation.
Someone mentioned the ferry system. They dock at Embarcadaro, about a 1-2 mile walk to Marina area. Flat, easily done. But the ferrys pretty much just run at rush hours.