I have family in the Bay Area and we just took a trip there with DS when he was 23 months old. It was awesome (but admittedly, he's a laid-back, adaptable kind of kid), aside from some wiggly moments on the airplane. Here's what we did while we were there that is kid-friendly:
- Golden Gate Park - ducks, paddleboats to watch, cyclists, other families, flowers, the Chinese Pavilion, the rose garden - it's all fun there.
- Chinatown - lots to look at, live animals in the fish markets (frogs, turtles, snakes in addition to the fish), dim sum restaurant was very entertaining for everybody.
- riding on the trolleys
Other fun SF stuff:
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Musee Mechanique It used to be under the Cliff House, but it got moved (luckily, as it was slated simply to close forever)
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Sutro Baths - fun to wander around in.
- You can rent bikes and go over the Golden Gate Bridge if the weather is nice, or just ride around SF.
-The CA Academy of Sciences would be fun if you keep an eye on his energy level.
- Chrissy Field is fun if you like to watch dogs running.
- The Pirate Store in the Mission has fun kid-friendly things, as well as bulk lard (who could ask for more, right?)
- Alcartaz or just riding around on the ferries.
- Pier 39 probably has lots of touristy but entertaining things going on.
Personally, I love using BART, and you can use it to get into SF from the airport, so you might not even need to use a taxi much if you can get around on BART, MUNI, the trolleys and streetcars, and on foot or bike. I would opt for not lugging a carseat unless you think he'd travel waaay better on the plane in one (but we were stingy, didn't buy DS a seat on the theory that if the plane's going down, a car seat won't save him, and just chanced it on the turbulence...) I guess I would minimize car travel - SF is a walkable city with good public transit. Take a lightweight stroller or a sling/wrap/ErgoBaby carrier...
What we did was to rent a car and used one they provided (but we were also driving all over creation visiting friends and relatives - if we were staying in SF, I would not rent a car unless the hotel has parking). I am happy to report that the one they gave us was VERY new (manufacture date of 03/09 and we were there in 06/09) and totally clean.
I think if you talk to him about it beforehand, show him pictures and maps, talk about the plane ride, and keep an eye on his energy level, you would be fine - maybe plan for one outing a day with naptime factored in, keep things very relaxed and mellow so you can really be guided by his rhythms and tolerance for novel situations, have some days that are exciting and others that are more mellow, you will all do fine and probably have an awesome vacation!