Stop shopping at JoAnn
The best place to find quality fabrics is a quilting store. Unfortunately, you're going to pay top price for good quality flannel, at least $8/yard, but you'll get a top notch product as well. JoAnn doesn't carry quality fabrics, in general, and a serious quilter won't shop there.
I haven't found an online company that I really like, though I can probably get a name of good quality flannel for you from my stash downstairs. My favourite quilting store is Eddie's Quilting Bee in Mountain View, CA. He has an online store,
www.quiltingbee.com. I've only every shopped at the store (which is just wonderful) but Eddie is a great guy and I can't imagine that you'll have a problem shopping online. You can also always find great deals in the store. In fact, I'd trust Eddie's judgement when it comes to fabric quality and say that anything you buy from him will be of top notch quality.
Good luck!