Indeed - we’re planning on getting a membership shortly before it re-opens.
I visited some folks there as they were packing up aquarium gear from the Howard St. location. I feel bad for all the insane amounts of effort they’re going through to move their massive collections.
I second Musee Mecanique – I usually take people there of all ages and they all enjoy it, but it’s great for kids. It’s also free to get in and then usually just 25 or 50 cents to activate each attraction. It has fortune tellers like the one that Tom Hanks consulted in Big and other really cool stuff.
We spent a weekend in San Jose with my kids when they were seven and eight.
We went down to Monterey and saw the aquarium - very cool. They really enjoyed that and I’d put that on your list. I’ve been whale watching on the bay, but its a long, wet, cold day for a four year old.
The next day we went to SF - saw Alcatraz (which I wouldn’t recommend for your little ones - too scary - but my kids thought it was very cool), rode a cable car, walked around the pier - and by that time it was time to go back.
San Francisco is a big city, and while it isn’t difficult for grown ups to get around in, its a “park your car and grab the bus” sort of city that can make getting around INSIDE town difficult with little kids if they aren’t used to public transportation. Parking can be a major hassle.
The surrounding cities and areas are a little easier to day trip into (though I get lost every time I try to drive in Santa Cruz).
My only time in Northern California was five years ago (January 2003), but at that time, I had kids aged 6, 4, 3 and 1. My advice, regarding stuff already mentioned in this thread:
Alcatraz, especially if the kids are boys (you didn’t specify their sex). They won’t get as much as adults get, but they’ll still be fascinated by it on their own level. My kids (the big three, that is) still remember it. And of course, the ferry ride is fun in its own right.
Do ride on a cable car.
Do go on the Jelly Belly factory tour.
If you get down to Monterrey, do go to the aquarium, and they have a wonderful playground which I believe is dedicated to the creator of Dennis the Menace.
I was underwhelmed by the Exploratorium. The Tech Museum in San Jose was way above their level. The Winchester Mystery House pretty much bored them, fun though it is for adults.
Not yet mentioned in this thread:
A nice day-trip would be north on 101 through redwood country. I definitely think kids that age would get a kick out of driving through the Chandelier Drive-Through Tree in Leggett, Confusion Hill in Piercy, and an Old Faithful-like geyser in Calistoga.
Wow, you guys are awesome! All that stuff to do close to Stanford is great too, because that’s where we’ll be much of the time. We are definitely going to San Francisco, but if there’s stuff closer to home that’s great for when they’re not in the mood for a big trip.