Lots of auto trimmers will be able to replace the plastic rear window for you but its best to go to someone who has already done it and you can check the results of how they do it to see if you are happy with it.
You can replace your whole roof and frame with one from an 03-04 Boxster or you can get an aftermarket roof with a glass rear window and fit that.
Do a search on here and have a look at
http://sites.google.com/site/mikefocke2/thetop-itsmaintaince%26replacement