Yes. If the condition of the rest of your top is good, then why not replace just the window.
Option 1: take it to an upholstery shop - they will remove the entire softtop, cut out the old window and sew in a new window - the new window will be slightly larger than the old/original one. Cost $400-$500.
Option 2: do it yourself with one of these kits:
http://www.emiata.com/BoxsterWindow.htm
Cost $89+shipping, + elbow grease.
I haven't done either, but will probably go with option 2 when it comes time to replace mine.
Good Luck,
Larez2