There is a Aan Francisco forum where you could get some good advice on traveling to and from the airport, depending on how big your family is a taxi may be the best way.

The Bart, the public transportation out there, begins airport service at the end of this month, that will certainly be the lease expensive method to get into the city.

http://www.bart.gov/index.asp

I like the Hilton at Fisherman's Wharf.

Make sure you get some crabs on the Wharf, and you may wan tot get your tickets for Alcatraz in advance too, those tours sell out and you don't have a large window of time to go if you are only doing an overnight.

http://www.blueandgoldfleet.com/