Hi,
I live in the area and would suggest the following stores:
if you can only visit one - I would visit Southwest Decoratives 5711 Carmel Avenue NE. The will have the most selection of SW fabrics and a good overall variety.
The Quilt Works 11117 Menaul has a good selection and a very friendly staff.
Quilts Ole 4908 Corrales Road - good selection, but might be harder for you to find.
There is a quilt store in Taos, but I have not been to it. It is Taos Adobe Quilting. It is at the plaza area, so that might be easy to see.
Santa Fe does have a quilt store, but it isn't as unique as the others.
I hope you have a great trip.
Donna