North or West S.A would be my choice. Traffic may be an issue depending on worl locations. Helotes, is a great town, just next door to S.A.
I agree with everyone on the housing aspect. Universal City, Schertz, and Cibolo are great and just outside of SA. There are lots of good schools in these areas. The Stone Oak area has some of the best schools right now.
As for a physician that will delay vaccinations...that may be hard. I've worked for several pediatricians and I know of NONE that will delay or not give shots as the parents wish. My sister chose not to vaccinate her youngest. The closest doctor she could find is in Austin.