A bit late to this one..but we went to SF area in August 2008 for 3wks with a three yr old and a 12mth old.
We spent a few nights in SF then round two weeks at Donner Lake, (it's a small lake about two/three hours drive from SF - we have relatives there) it was great, lovely swimming and a small sandy beach though I think the beach was run by a club just for residents and their guests?)
We did a couple of day-trips out to Lake Tahoe too which was also nice and a ride up to Heavenly Ski resort, which was a fun ride in cable car for the three year old and the views of the lake were stunning.
We did a couple of nights at Monterey Bay to see the world famous aquarium (that is fantastic - highly recommend it!) and a drive along the Big Sur with a stop at Carmel which is all very pretty. I would like to have gone on a whale watching trip from Monterey but it wasn't practical with such young children (very early start, several hours on a boat and no guarantee of seeing anything!)
Alcatraz was a great day out, the audio tour is brilliant, very atmospheric, there are good views of the bay - we didn't book though, just turned up and paid at the kiosk an hour before - perhaps we were lucky?
Some of our party went on a trip down the Truckee river near Donner including my 3yr old (I stayed behind with baby!), I hear it's quite tame (certainly not white water rafting!), so depends on how old your son is, but the kids in our group liked it, they give you water pistols to squirt at each other etc.
If you visit Donner Lake and your Son likes a little Horrible Histories type stuff, you can go to a museum to learn about the tragic "Donner Party' (Google it!) It's a good way to learn about how incredibly tough the lives were for settlers back in the days of the gold rush etc... Anyway, I am rambling, sorry! Hope this gives you some ideas...