Besides the all-manta store in Ajijic across the street from Farmacia Guadalajara and the store gogirl posted in Chapala, there are no other fabric stores lakeside. The closest going to Guad is Textiles Capilla, a fabric warehouse where fabric is sold by the kilo. The fabric is mostly stacked high on pallets. 99% acrylic. This is on the highway to Guadalajara right after the La Barca highway. Watch for the Pepsi plant on the right and the warehouse is immediately following on the road that exits to the right.
After that is Guad Centro near the Cathedral. A couple of dozen stores, all acrylic.
For natural fabrics, there are two main ones. One is Centro Mercantil Villanueva on Pedro Buzeta street in Santa Teresita. There is an all-cotton store near there but I don´t have a name or directions. Those things are on a card somewhere. If I find it, I´ll post it here. Then there´s Telas Al Puerto de Veracruz, Avenida Chapultepec No. 125, Colonia Americana, CP 44160. Moreliana says it´s the best fabric store in Mexico. There are other smaller fabric stores along Avenida Chapultepec.