Go with your gut. A dive shop would be stupid to make you feel unwelcome if you bought gear and training elsewhere and later walked in their door. If they do that, (down the road) it is a good reason to avoid them.
I would avoid a shop that sells exclusively scuba pro, even though it is quality gear, it is often not a good value in my opinion. I have lots of USED scuba pro gear.
If it is narrowed down to two shops, it might be instructive to find out the exact costs for everything - basic gear, course, certification card, pool fees, open water dive fees, book fees, online training fees or any other fees they can come up with. If you get the feeling they are playing games, then I would pay attention to that fact.
Lastly, I would just ask how long is the class? If they emphasize it is super fast, quick and easy... well I would probably pick the shop that doesn't want to emphasize the shortness of the training. Busting balls over EXACTLY HOW they are going to train you is going to be a challenge without coming off as an arrogant know-it-all , especially since you (don't yet) know much of anything.
There can be some significant benefits to patronizing a particular shop and having them know you. However, realistically, you will not know what is the best shop for 6 months and after you have been certified, so don't sweat it too much.