Where to stay? What's you budget?
If you can afford high-end, stay at Valencia, La Mansion, or Watermark. Hyatt is also nice. Avoid the Hiltons. The Marriotts ON the Riverwalk had not-so-good reviews from a couple of folks I know, Marriott Plaza fared better. The Menger has ghosts (well, supposedly). St. Anthony and the Sheraton Gunter are right downtown, too, and both have a bit of history about them. You'll pay a premium for parking at the Riverwalk/downtown hotels. At the lower end, there's a plethora of hotels around. A couple of B&Bs in town, too. The Doubletree near the airport was formerly a part of the La Mansion family, I don't know whether they've refurbished, but when I stayed there several years ago it was very much different than your run-of-the-mill Doubletree.
Food? My fave was a neighborhood place, La Fonda on Main. Really nice folks there. There are several "nice" places just off the Riverwalk, but most of the spots on the Riverwalk are tourist traps. Outside of downtown, Cappy's, Paloma Blanca, Caparelli's, Silo, and a few others make up a pretty good collection of restaurants. A bit out of town is Rudy's Barbeque. I like Rudy's, and I like Busbee's in Bandera. If you drive in from the north, make a stop at Salt Lick south of Austin (cash only, please).
Oh, see if you can get an evening at The Landing jazz club on the Riverwalk. Jim Cullum doles out traditional jazz - that's where they record the PRI radio series "live from the landing".
In the area: we all know about the Alamo - it was one of a string of missions along the San Antonio river. I actually find some of the other missions to be much more interesting, and far less touristy than the Alamo. It's worth a couple of hours to see them. Wave at the planes in the pattern at Stinson as you tour the missions (two of 'em are under the pattern for 14...)
More as I have time.
San Antonio is a great place to visit....