Here is a link to many of the quilt/fabric shops in the area..
http://www.quiltart.com/lancaster.html
My two favs are #11 - The Old Country Store. They are under new management since the last time I was there but I'm sure it's still a great shop. There are a couple of others right there as well. It's also in a nice little 'village' setting.
Next is #18 - Quilt & Fabric Shack in Bird-in-Hand. Not far away at all. They have the largest flannel selection of any shop I've ever been. Very good quality fabrics all around.
Just remember, most - if not all, of these shops are not open on Sundays.
Enjoy your trip!