There is no single best shop. For the most part, certain places are best for certain things. For hops, it's usually best to hit up either a hop farm or a hop retailer. Hopsdirect, freshops, nikobrew, and yakimavalleyhops are all really solid choices. Grains are trickier if purchasing large quantities. Morebeer does a bit better than most, selling 5 and 10 pound increments for a fair price, and free shipping over $59. But if you're buying a pound or just a couple ounces of something, shops are all pretty much the same. Custom false bottoms, or one off custom stainless parts are best purchased at norcalbrewingsolutions. For general brewery equipment, just follow the sales. Get on everyone's email list, and read all the stuff you get sent. Sometimes you'll find a steal. Wine kits seem to be cheaper, (even with shipping), from homebrewsupply.
Service, I've found, is very good no matter what the shop is. After all, most of these places are owned and operated by people just like us, homebrewers trying to scrape together a living in between mowing the yard and going to your kid's baseball games.