I love Stitch N Frame, Whittle's, and Crafttown for their fabrics and good prices. I've also ordered from some of the places mentioned in the above posts.
Sometimes when I find a fabric I like, I go to the www.quiltshops.com website and enter that fabric into the search bar to find the best price. That site is a fabric search engine for over 200+ fabrics.
I've also used Quilt Fabric Closeouts for discontinued fabrics. Many times, the fabrics she has listed are still current in many other quilt shops.
I agree that it's the manufacturer more than the quilt shop, but it's also about the prices, good service, packaging and shipping as well. Are they reasonable in their shipping prices? Do they ship promptly? Are the packages well-wrapped and protected from the weather in case they're handled roughly?
I really try to find fabrics on sale or discontinued to save money. That's one of the reasons why I like Stitch N Frame. They have a weekly sale email that goes out on Wednesday. If they carry something you really like, if you wait awhile and check those sale emails, you will eventually find it marked down.