There is the Aquarena Center with a glass bottom boat ride.
Of course, shopping at the Outlet Malls - I recommend that you do this during the week (it is so crowded there on the weekends)
Wonderworld Park is fun too
Drive to Gruene, Texas nearby - I love this little place
Drive to Austin - the Austin Children's Museum is free on Wednesday from 5-8.
If you like water there is Schlitterbahn Water Park in New Braunfels
That's all I can think of
Enjoy your trip! I would love to get out of town...
I lived in Austin a few years ago so I hope my info isn't hopelessy out of date. I would definitely drive to Austin, since it's only about 30 minutes from San Marcos. Zilker Park has (had?) a small train that went around the park that was really fun. You could also go swimming in the Barton Springs pool which is fed by a natural spring and is really cool. It's in the same park as the train.