If the rest of the top is in good shape, often you can have a boat canopy specialist stitch in a new window. I think that's usually around $400.
If the top is trashed, you can try and get a top from a 2003 MY boxster - but you have to get all the hardware as well as the fabric, as they changed the structure to support the glass window.
Another option is to get a GAHH (
http://www.gahh.com/) top, they have a glass window, but do not require new hardware. Unfortunately they limit engine access somewhat.
-james