Marshall's Dry Goods sells rolls of batting. They have their brand MDG too and most LAs in my area buy that.
Hobby Lobby has Warm and Natural batting by the roll on sale for 40% off every other week.
For single sizes I buy from Missouri Star, stock up when it's 30% off.
Pellon natural cotton batting is sold at Walmart in packages. I use that for donation quilts.
Connecting Threads has different brands of batting. I buy the wool and silk batting from there when I want to use those in a quilt.
I have always found better prices somewhere else other than Joann's most times.