The best shop might also depend on your goals in diving. If you are interested in tech, I would recommend 5th Dimension on Alki. Mark is incredibly knowledgeable, and can tell you everything you will ever need to know about the sport. He also has great prices. Even if you aren't interested in tech, I would still recommend the shop, although I have a feeling that those not interested in that aspect of diving might feel a little intimidated/alienated upon entering what with the dozens of doubles, stage/deco bottles, DPVs, etc lying all over the place. If you do go, just be sure to strike up a conversation. Mark is generally pretty silent, and won't say much unless you say something first. At least that's how he is with new customers/people he doesn't know. And if you are there during the week, you just might run into me since I practically live there when I am not doing school work =P
Another shop I would highly recommend is Underwater Sports Bellevue, with emphasis on the Bellevue part. While, I cannot recommend the chain as a whole (stay as far away from the Seattle store as possible), I can tell you that Doug (again, Bellevue store) knows how to run a damn fine shop! I can't count the number of times he has been willing to bend over backwards in order to help me out with something, even if he was already swamped with work, and my request required immediate action (such as a spontaneous VIP that I needed done within the hour). Every employee in that store is great. The major downside to that store is that they have to send gear out to headquarters (the Seattle store) in order to get it worked on since they do not have space to do it in their own shop. They ship gear to them every Wednesday I believe. But their great service is something that is extremely hard to come by these days, so I would say it more than makes up for the lack of a repair space.
As far as gases, 5th D offers the works (Air, EANx, O2, He, and Argon), and UWS-B offers Air and EANx only (up to 40% I believe).