You can order the material from sailrite.com. It's called vinyl window material, one quality brand is strataglass. You want min 30 mil, 40 mil is even better. Any boat canvas shop can replace the windows for you, or you can do it if you have a heavy duty (walking foot preferred) sewing machine. Sew the new window on, then cut the old window material out. That way, you don't lose the shape and handling the material is easier with the old window still in place.
Check this page:
http://search.sailrite.com/category/...-crystal-clear