To avoid parking fees, Bay Bridge Toll fees, and traffic all in one fell swoop, my recommendation is to hop on a "Daly City" BART train @ the Fremont station (Approx 30 min drive from your Hilton Garden Inn Cupertino) and take all the way to Powell St. station in SF. Fare will be around $6 each way. Then, hop on the cable cars (Just outside BART station) to the wharf which is approx $5 each way or you can buy a "Day Pass" for $13 which also includes buses and street cars down by the Wharf/Pier 39. I try to avoid driving into SF as much as possible thus why I heavily rely on BART when I visit.