Depending on who you are traveling with and their tolerance for a detour... As you come into NYS, you'll go into Binhamton. If you take 17 West, you'd go into Owego (about 20-25 mins from Binhamton), home of Patchwork Angels. From there, 96 N to Candor (about 15 mins from Owego), home of Pucky Huddle. Continue on to Ithaca (maybe 15 mins)and Quilter's Corner. Then Route 13 back to Cortland and Route 81, 20 or so minutes away.
If that's too much of a detour, Route 81 will take you through Syracuse. In the Syracuse area I know of the following: Patchork Plus in Marcellus, Mission Rose in North Syracuse, and Calico Gals in Fayetteville.
I've not been to Mission Rose, so can't comment on their shop. I enjoyed all of the others, probably the ones in the Southern Tier more than Calico Gals. Patchwork Plus is also very nice; it used to be in Skaneateles but moved a year or two ago. Calico Gals is very small; it's in a converted barn. They occupy the upstairs and the downstairs is a very nice needlework shop. Not far from it is Green Lakes State Park, very pretty with a small beach, rowboat rentals and a couple of nice trails. Just suggestions to occupy other family members' time while you shop!
Good luck, hope you are able to find something that will work for you.