Hyatt Wild Oak Ranch is over the highway from Sea World and it is awesome. Every room is a suite and mini kitchen/bar. WOR has an arcade, gym, family style TV building - all that over looks their huge indoor pool and outdoor pool and their 2 ridiculously HUGE waterslides. And their lazy river is awesome. There is a "beach" on one side with a bar that serves umbrella drinks for the grown ups and slushees for the little ones, and on the other side they have seating/tables and private cabanas (first come first serve) dotted along the river. They have nice landscaped grounds to walk/run/hike. There is also a kid's camp clubhouse where you can drop your kids off for art time or camp time and the parents can go off and do their own thing, as well as a nice play area. There might be one or twofamily friendly things I'm forgetting! On choice nights they have an outdoor family movie night along w/s'mores time in their outdoor fire pit. It is very family friendly. All that activity though...you might have time to enjoy them if you will only be there for 2 days, with most of it spent at SW.
Ifyou want historic, I suggest the Emily Morgan, the Crockett Hotel or the Menger Hotel across from the Alamo. The last time I stayed at the Menger, it was at least $150/night. I've stayed at all 3 and they are all very very nice. Although they are in town and you'll have a 15+ min drive to SW, it might be worth it b/c each hotel has its own place in Texas and San Antonio history.
If you are looking for something non-resort, non-historic, I've never had a problem staying at either Marriott hotels right on the Riverwalk, and thru priceline.com I've probably stayed at each for maybe $100 or less a night.
Don't stay in any hotel near the highway and Marbach (sorry for anyone who lives in that area) but I used to live near there and that place has gone down in value and safety, imo.
hth