You can get polycarbonate glass at hardware stores and home centers. There are several different formulations but the kind that you get there will be a little different chemically than the name brands like Lexan (r) and I think that these are much better. You get them at specialty plastics stores. Most codes say that you must not use real glass in storm doors and windows next to doors, or if you do, it must be tempered. Therefore, this is a commonly available.
The next question is why the birds are flying into your windows. I have seen it where it looked like they could fly in one window and straight out another and where they could see a reflection of themselves and thought that it was an intruder on their territory. However, in both cases, I never saw them hit hard enough to break the glass. You might check with a local birders group or Audobon Society, or even a store that specializes in bird houses, food, etc. to see if they have any suggestions. Henry