FWIW, although Lexan is theoretically stronger than Plexiglass, it will shatter a lot like glass if struck hard enough, whereas Plexiglass will usually just crack. Initially Lexan is clearer than Plexiglass, but Plexiglass doesn't discolor quickly if left outside in the weather; Lexan will tend to yellow after 5 or 6 years outdoors. Scratches can be buffed out of Plexiglass; Lexan scratches are more permanent. Whether that makes Lexan unsuitable or more suitable for airplane windows, I don't know.
If your plan is to just buy whatever, Plexiglass or Lexan, by the sheet and cut it, I can say unequivocally that Lexan is a whole lot harder to work with than Plexiglass. You'll need a very fine tooth saw to work with Lexan, and even then, it's easy to shatter with a power saw blade.
I think it would be better to get your windows from an aviation supplier. You might still need to do some minor trimming, but my guess is that the results would be more satisfying.
Cary