Well, technically this isn't a store, or isn't only a store but I couldn't think of a better category.
The Biblioteca should be your first stop. The Biblioteca is the largest English library in San Miguel, and I think the second largest in Mexico. It is chock full of helpful English speaking expatriates that want to talk to you and help you. I think part of their desire to chat must stem from the need to talk to new people as in my month in San Miguel even I got quite tired of running into the same 6 people over and over and over and... well you get the idea.
Anyway, the Biblioteca sells tour books and maps of the city (and other things) - and is also a library/educational center/restaurant/great spot to sit and do nothing.
Go to the Biblioteca your first day and buy yourself a map. Some of the streets change their names from block to block so a map is a most helpful thing if you plan on getting somewhere other than by happenstance. For example - the street Prolongacion Aldama becomes the Canadita de los Aguacates which becomes Recreo, except that if you make a left off of Canadita you wind up on Prolongacion Aldama again which then becomes Aldama, jogs left and becomes Cuna de Allende then Hidalgo which then turns right and is called Calzada de la Aurora. How do I know all that - because I still have my map.
The tour books they have in the Biblioteca are quite good, some excellent. I looked around bookstores at home before my trip but there was never more than a page or two on San Miguel. Amazon.com had a book about San Miguel that they said was out of print - that book was available for sale in the Biblioteca. They also have lots of books on walking tours of the town and surrounding areas.
The Biblioteca also sponsors tours - the money from which goes to children's education. The house tour is what they are best known for and it takes place every Sunday morning. I hated it more than you can possibly imagine. They also have tours of the city that are much better. My tour was given by an elderly American gentleman (but don't tell him I said that he was elderly) who knew everything and everybody. It wasn't the best tour I've ever been on in my life but it did give me a good overview of the town and how to get around it.