You can get glass for baffles at Cheap Pete's or any other framing place. I believe they have reasonable prices if it just happens that the baffle sizes are the same as their precut glass.
Otherwise, they could probably cut glass for you.
However, acrylic is much easier to work with. Depending on how long these baffles are, you may require thicker acrylic to prevent bowing. I believe Home Depot only sells the thinner acrylic.
Acrylic on glass can work fine for some purposes. As long as you don't expect your baffles to be completely waterproof and just need the baffles to stop bubbles, then many people have had success using silicone to affix acrylic baffles to a glass tank.