I've got lots to choose from locally! Well, within an hour.
Ivy Thimble in Victor is great, a good mix of fabrics, wonderful staff. They organize the retreat I've been going to for several years. Also offer fantastic longarm service.
Material Rewards in Dansville, focus more "traditional" (Kansas Troubles, Thimbleberries), but a good selection overall.
Patchwork Plus in Skaneateles was featured in the most recent edition of Quilt Sampler Shop Hop by BH&G.
Mt. Pleasant in York - great selection, fat quarters of most fabrics are always available.
O'Susannah's in Watkins Glen. Not huge, but very nice. Friendly staff. Upstairs quilting room that can be rented out (I swear I'm going to do this someday!)
Hoover's Shoes aka Golden Lane in Himrod. This is a Mennonite store, you won't find LQS atmosphere, but fabrics are less than $6/yard. Same fabrics as LQS.
Edgewood, another Mennonite store. Not as much fabric (they also sell general dry goods), but what they have is also at a fabulous price.
There are others, but these are my favorites. In August, younger DD goes to college in Buffalo - which means I'll be traveling near Aurora Sewing, another shop I enjoy but that is generally a bit farther than I travel. In addition, if I want to add another half hour to hour, I could give you several more great shops - Pucky Huddle, Churn Dash, Village Sampler (also carries cross stitch), Quilter's Corner...
Do you need any more reasons to visit upstate NY??