Pioneer Farms, my parents took me there twenty years ago as a kid, and it's still around. Its a living history type place, learn how pioneers and native Americans lived back in the day. I think they even have cotton fields out there if you want to send your kids out there to ware them out before you take them home
We drove through there and stopped for a few hours at the Nature and Science Center. It's really awesome for smaller kids. We could have stayed there all day. The dino pit was my kids favorites (5 and almost 3). They can dig and play in a giant sand pit with "Fossils" all over it. There are tons of other educational things all over, but we weren't in the center long enough to get to explore much of it. It is inside of a really nice park where people were picnicking and running on the trails everywhere. Really very nice.
I have taken my kids to the Bob Bullock museum. Very interesting and informative.
Not sure if its available at the Bob Bullock museum but when I was at the Dallas king tut exhibit they had these hand held wands that would give you extra information of the exhibits. If they are available, its worth the extra fee.
The McKenna Children's Museum in New Braunfels is bigger and better than the downtown Austin Children's Museum. It's a bit of a hike from Austin, but my 3 yr old (at the time) loved it.