Phantom of the Attic has been around forever, and it's always been very accomodating to gamers. It's accessible if you live or work downtown or know your way around the city. The owner Jeff is a great guy, too: knowlegeable and friendly. Legions Games has probably become the most popular store in the area, though. It's located in the northern suburbs, but very easy to get to from virtually anywhere. A huge selection of product, good staff and owner, and a gigantic open gaming area with tons of tables for pretty much any nerdly pursuit.
PM me if you'd like more info on either place