You may be in SA around Fiesta time - check the previous post for a link to find free (or cheap or whatever) events. Some are very kid-friendly. Many are quite crowded. If I could pick only one event to go to this year, I'd check out Battle of the Bands, just b/c it has been so long since I last went and it was always a treat
Tuesday afternoons many SA museums are open free to the public.
Just north of San Antonio is the Natural Bridge Caverns
There is a great park and playground in New Braunfels (off I-35 between San Marcos and SA): http://www.newbraunfels-tx.net/
(this site has more info on other area attractions).
The New Braunfels children's museum is opening or just opened:
The mission trail in SA is fun.
Austin has lots of great parks and isn't too far north of San Marcos, if you are interested. Check out the bats!
(no idea when the best time is to go see them - but give these guys a call, maybe?)
You may still be able to catch some wildflowers blooming in the hill country, though it has been a screwy season for it. Or the Lady Bird Johnson Wildflower Center is in South Asutin for a look-see.
That's all I can think of off-hand that hasn't already been suggested. Enjoy!