Oh.my.gosh. Not only did I take a toddler on several vacations in the Bay Area, as a stay-at-home I also raised a toddler in the Bay Area--in San Jose, to be exact. I am an EXPERT on how to keep your toddler entertained in San Jose.
Of course, you'll want to do Muir Woods and Stinson Beach. The Monterey Bay Aquarium is a fun thing to do, too. But they're all about 2 hours away from San Jose. You might want to go over to Alcatraz Island, too. They have a very interesting tour where everyone wears headphones. I brought a Walkman* loaded up with Wee Sing songs and a pair of comfy headphones for Sam. He thought that he was taking the same tour that ExLax and I were taking, and he enjoyed it immensely. (*I suppose today you'd load those songs on to your iPod and slap a comfy pair of headphones on the kid. I'm showing my age here as Former Toddler Sam is now a sophomore at San Jose State University.) While you're in SF, you might as well take your kid on the cable car ride since they're unique to SF. Go see a winery or two. The wineries in the Napa Valley are nice, but Kendall-Jackson is right off 101 in Sonoma County, just north of Santa Rosa in a little town called Fulton. You could do that winery in the same day that you're doing Muir Woods and Stinson Beach. Be prepared to have alternate entertainment for your kid--like headphones loaded up with kid tunes and a container full of Cheerios.
Here's what the locals do in San Jose:
Happy Hollow Park and Zoo: This place has a cute little zoo (It's not like the San Diego Zoo, so don't be disappointed because it's cute and little), a playground for the kids, and kiddie rides, including Danny the Dragon. You'll pay to park, and the admission fees will be expensive, but your toddler will LOVE Happy Hollow. I understand that Happy Hollow has recently been renovated, and the petting zoo may be gone, but this place is a toddler's paradise.
Children's Discovery Museum: I took my kids here a lot, and then the schools took them on field trips to the Children's Discovery Museum. There is a real fire truck that the kids can play on, there is a bubble room, a water play room, an art room (make the corn husk dolls!), an ambulance room, a supermarket room, and lots of places for kids to engage in interactive play. My kids liked this place. I LOVED this place!
Emma Prusch Farm Park: San Jose used to be a farming town before it became Silicon Valley, technology capital of the world. Emma Prusch Farm still has the barns with small farm animals (turkeys, peacocks, chickens, goats, rabbits, pigs and cows), the orchards, gardens and original farm house. It's a great place for city kids who've never seen a real farm. This is one of the places that the kids and I went on school field trips. This attraction is free. You might want to take a picnic lunch and enjoy sitting out on the huge lawn. Your toddler will enjoy the playground.
Christmas in the Park: Depending on when your cousin is getting married in November, this attraction might be open. The Plaza de Cesar Chavez in downtown San Jose is filled with Christmas displays. They're usually set up the Friday and Saturday following Thanksgiving. Our PTA always set up a Christmas tree or two in the park, and I've spent much time down there decorating our school's trees. The commercial exhibits feature moving displays. It's fun to go at night. They even set out a snow machine that blows out fake snow made of soap. Also, the ice skating rink will be set up right there across the street from Christmas in the Park and you can skate under the palm trees. They have ice skates that fit toddlers. (Note: I never strapped on ice skates, but I took my kids to this thing a lot and they enjoyed skating while I watched.) In the summer, the fountains in Plaza de Cesar Chavez shoot off from the plaza and the kids run through the fountains. It's great fun for them.
The Tech Museum: I'm stretching it here a bit because your toddler will likely be bored out of his or her mind at this museum because it's tech heavy. You and your husband will love this place. I'd do the slap-the-headphones-on-your-toddler's-head trick and take the kid through the museum anyway. The Tech is across the street from Plaza de Cesar Chavez in downtown San Jose. They have an iMax domed theater which all of you will enjoy.
There are lots of parks with playgrounds. Vasona Lake Park has the Billy Jones Wildcat Railroad, and there is a cool carousel there, too. It's over in Los Gatos. San Tomas Park in Campbell has an outdoor water play feature. There are tons of parks in San Jose. If I knew where you were staying, I could recommend nearby parks.
I'm not suggesting the Winchester Mystery House. It's overhyped, and with all of the stairs you'll climb, it's not fun with a toddler. Trust me on this.
Feel free to PM me and I can give you more suggestions, depending on the part of town you're staying in and what your itinerary looks like. If you need a babysitter, I can hook you up with one of those, too. I might even be able to hook you up with a designated driver (Former Toddler Sam doesn't drink, and he has a car).
The places you listed above probably are, or would be of more interest to a toddler than the aircraft ride I referred to. I suppose those are of more interest to an adult. 
