Make reservations for Alcatraz in advance or it's unlikely you'll be able to go when you want. Walk out onto the GG Bridge, especially if it's a nice day. It's the best way to appreciate the sheer size of the span.
If you've made no hotel reservations yet, try to avoid staying in the City itself. It's either way overpriced or so nasty that you wouldn't want your 4th worst enemy staying there (1-3 would probably deserve it). I usually end up staying closer to SFO in one of the moderately priced hotels. Also, looking across the Bay in Emeryville or in Marin County would be decent as well. Remember you will pay tolls on every bridge, including the $7 electronic toll on the GG Bridge (google 'GGBridge' toll to find out how to pay for those).
Having a little one will make some of the sight-seeing more difficult, but there are still plenty of places to visit. There are lots of park and beach areas around, including Baker Beach, Ocean Beach, Crissy Field, Golden Gate Park, etc. Muir Woods in Marin is fun also, plus Rodeo Beach and Point Bonita in the Marin Headlands, just across the GG Bridge. The Embarcadero is a nice area to walk (as long as it's not overly crowded). You get to see the wharf area, which will take you down to Pier 39 if you are inclined to go there. It IS a tourist trap, but you can certainly find souvenirs galore there.
Twin Peaks offers the best views of the entire city, including the GG Bridge, Bay Bridge, downtown, the Bay, Oakland, etc. Absolutely worth looking up how to get there for a little bit. It's spectacular at night as well. There are countless museums in and around San Francisco. Some are worth it, some not so much. A list of what you'll find:
http://www.baycityguide.com/museums.html
I am not that familiar with San Jose or the South Bay, in general. If your focus is going to be SF, don't stay all the way down there or near Santa Cruz. If those areas are what you're planning on seeing, it would be great. Otherwise, you're spending too much time in the car. Not fun if traffic is heavy (which it frequently is).
If shopping is the wife's thing (or yours, for that matter), you might want to spend some time around Market Street in SF from Powell to the Embarcadero. Lots of department stores in the area and fun to walk around. Emeryville has an upscale outdoor mall as well, with an Ikea at the far end of it.
Don't be afraid to take BART places, but it only travels southwest-northeast in SF itself, but will get you to SFO, Berkeley, and Oakland (other places also).
Also, be prepared for different microclimates everywhere you go. That means bring clothing that will allow you to prepare for anything. It can be quite chilly in the City, especially near the ocean. But you can drive across any bridge for about 15 minutes and temps can jump 20 degrees. Keep an eye on the weather forecast so you know what to pack. Finding a local tv station's weather report will show you expected temps on the coast, on the Bay, and inland. Shorts are still usually good for time spend away from the ocean. But jeans will be appreciated as well as sweatshirts/windbreakers for the chilly areas.