Since you've got glass in good shape I'd most certainly reuse it.. all the other replacement options will eventually go opaque with time. even Lexan, and while strong it's remarkably easy to scratch.
We've had success replacing the gasket seal with aluminum-framed ports with Dow Corning 795 sealant. Save some small pieces of the orignal rubber to center the glass in the frame. Mask off the glass and the frames to ease cleanup after it's all assembled.
Good luck.. it's pretty nice to eliminate window leaks!
".. there is much you could do at sea with common sense.. and very little you could do without it.."
Capt G E Ericson (from "The Cruel Sea" by Nicholas Monsarrat)
1984 Fast/Nicholson 345 "FastForward"