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It sounds like most people have the touristy stuff covered but I'll put in two cents (fore-warning, I have no idea what a 9 year old might like so I'm just picking the kid friendly stuff I can think of):

Oakland vs SF
- SF has more to do, especially kid friendly stuff, but all of it costs $$$
- Oakland is maybe my favorite spot in the US, but it is fairly rough in a lot of areas and outside the nightlife there isn't a ton to do. Good food spots. I would recommend staying in Oakland or Berkeley as it will be a LOT easier to get to the Warriors game. Getting out of SF and crossing the Bay Bridge can take an hour+ during rush hour. As well, getting into SF via ferry or BART is incredibly simple and usually cheaper than parking.

Other touristy/not touristy things to do not mentioned
- Jack London Square (kind of neat, good place to stay in Oakland for a safe, comfortable feel)
- Ferry Building (as an added bonus, take the ferry from Oakland at Jack London Square to the Ferry Building in SF. It's got a great icecream spot and just taking the ferry is nice, kids seem to love it)
- Embarcadero/Boardwalk (my recommendation: you can actually walk from the Ferry Building to Pier 39/Fisherman's Warf. It's about a 30 minute walk, maybe 45 if you're going slowly. You can hit the Science museum [exploratorium] on the way for a fun break. This also allows you not to have to pay a significant amount of money to park near Pier 39. The Alcatraz cruise spot is also between the Ferry Building and Pier 39).
- Coit Tower (nice lookout spot/tower. You can walk here from the boardwalk)
- Baker Beach (decent beach, amazing view of the Golden Gate. Do not walk TOO close to the north end, it becomes a nudist beach and there's almost always some dude trying to get his dick in the background of people's pictures).
- Ocean Beach (a little nicer than Baker, usually lots of surfers)
- Golden Gate park (SF, you can spend an entire day here walking around, do not underestimate it's size)
- Tilden Park (drive around the Berkeley Hills for a cool drive, Tilden Park has some great views and a steam train which MIGHT be too young for 9, but he might get a kick out of it. Doesn't run every day though so make sure before you make the trip)

Cool neighborhoods/areas in SF
- Chinatown (vibrant, amazing, best Chinatown in the US)
- Union Square/Market St (cool if you want to walk around in a super safe area of downtown or have anything you need to buy)
- Mission St (good taste of mexican culture in SF)
- The Castro (good taste of gay culture in SF, walkable couple blocks, nice area, nothing TOO risque but not for the very conservative)
- Haight-Ashbury (I cant see much value here for a 9 year old... but they do have a Ben & Jerry's!)


If you have a car and feel being nature-y
- Tennessee Valley (north of SF, nice little hikes, cool alcoves and beaches)
- Point Reyes lighthouse (north of SF, amazing drive and cool view for whale watching)

Places to eat
- Noodle Theory (asian, Berkeley)
- La Taqueria (mexican but get the burrito, SF)
- Brown Sugar (breakfast/soulfood, good waffles, better w/ chicken, Oakland)
- Home of Chicken & Waffles (also breakfast, walking distance from Jack London)
- Homeroom (macaroni & cheese, super good variations, def kid & adult friendly, Oakland)
- House of Nanking (asian, SF)


My recommendation: avoid Pier 39 like the plague. It's awful. Just a noisy tourist trap that is geared towards you spending money. There really isn't much to do, so if you must, spend a half hour. The walk to it from the Ferry Building is great. Alcatraz is a must for a kid. Golden Gate is cool, but it IS just a bridge at the end of the day, so I might recommend doing Baker Beach or something and getting a great view. If you do Tennessee park or Point Reyes, you can get there by crossing it so you get the "full experience" (which is overrated).

Stay in East Bay, make day trips to SF, that's my recommendation. Regardless, I'd stay close-ish to the Bay Bridge on either side. Do not underestimate the time it takes to drive around SF. If you stay near Union Square in SF, for example, it's about 30-40 minutes to the Warriors arena, in rush hour (conveniently the time right before a game) that can go up to 60-70 minutes, even 90 minutes on a game day with no accidents). Wherever you stay, prepare yourself for the time. And remember that the Bay Bridge and Golden Gate are both tolls going into SF.

Also there is a cool self-guided mini-car tour you can take. There are these little yellow cars that seat two. You get helmets and zip around some neat spots in SF. I've never done it, but I know people who have enjoyed it. You can get them near Pier 39 I think.

EDIT: I agree with everyone on dressing. Pants, shirt, fleece, wind breaker, rain jacket, hat, sunscreen. Layer! It might be super hot, it might be cold. It might pour rain, it might not. You won't need a heavy jacket, but couple removable layers are essential.

If you (or whoever else) have an questions you can PM me, I've spent a good amount of my life in the Bay Area.