You can go to any glass shop and they will cut the glass for you. I used glass baffles when I first built my sump, but when I decided to expand my refugium, I went with acrylic as it was readily available at my local Lowe's.
People recommend glass for baffles because silicone (what you will use to attach the baffles to your sump) does not adhere to acrylic, but it does to glass. From my experience though, the acrylic baffle to my refugium has been holding up very well for about 8 months now. If you go with acrylic, don't skimp on the silicone.