Lately, I've been confining my shopping trips to quilt stores to when I'm traveling--chalk it up to burn out on my own local quilt shops and a healthy stash.
For online purchases, I use Keepsake Quilting, Fabric.com, equilter, Burkholder Fabrics. If I'm hunting for an older fabric that I need more of, I do a web search and will buy from whatever little shop may still have some left. I did this recently and bought from a shop in North Dakota and a shop in Idaho. They were very nice and helpful.
I avoid purchasing fabric from big box retailers because I've found the quality of greige goods available in that setting to be inconsistent, at best. I'm sure there are many who've never had issues with fabric from big box stores, but for me, I'm not willing to take the risk.