From either airport, you'll be making a connection.
Outside of doing something exotic, you really have five options:
- Southwest, most likely connecting in Orlando (but possibly in Tampa or Fort Lauderdale): Two free checked bags each and if you care where you sit you can pay for the early bird check-in and most likely get an A boarding pass.
- Jetblue connecting through either Ft Lauderdale or Orlando: Some fares have one free checked bag/some don't. Free in-flight wifi if that's important to you (though on many of their older planes you'll lose connection out over the Gulf, depending on routing, and also over the Caribbean). If you need leg room, their even more space seats do actually add some leg room.
- American connecting through DFW or Miami. Unless you're a frequent flyer with them or have their credit card, you'll pay for bags. If you need more leg room, you can pay for their Main Cabin Extra which will come with a free alcoholic beverage and snack. If you have an Amex Platinum (or Centurion) card, you can also use the Centurion Club in either DFW or Miami, which would make your layover somewhat nicer.
- Delta connecting through Atlanta. Basically the same drawbacks and benefits as American except if you do have an Amex Platinum, you could use the Skyclubs in both Austin and Atlanta. Their upgraded economy product is called Economy Comfort and also comes with a free alcoholic beverage and drink.
- United connecting through Houston (IAH). Same as American/Delta except that their economy plus product doesn't include the drink and snack.
You could book any of the latter three today. You'll have to wait couple of months for Southwest and JetBlue.
Southwest is likely to be cheapest all-in unless you have a way to get free checked bags on one of the others. Looking at last May and at the March schedule it looks like Austin will give you a lot more flight options with them than San Antonio.
If you do book Southwest, keep an eye on the connection point. They do offer connections at BWI (Baltimore-Washington) between Austin and San Juan, which is more than a bit out of the way.