[Overdrive]

As has been mentioned already, you can always go with a new top with glass instead of the plastic. The downsides to it are a smaller window that may restrict your rear view, and the glass will not fold like the plastic when putting the top in the service position. If you're ok with these two things (many people have been), and your original top could use a replacement, it's worth the cost. Just so I make sure I say it though, understand that you can't put glass into your original/current top that has a plastic window. It's a complete replacement of the canvas top.

As for the plastic replacement route, some places will do it, some places won't. Some won't stitch it in with the top on the car (hence your high overall cost due to labor for removing and installing the top), and others won't stitch it in if the top isn't on the frame for them to ensure the window doesn't sag. But as others have said, it does seem possible to have it done, just make sure it won't leak and that your top isn't looking bad overall, otherwise you might as well pay about the same and replace the whole thing with a new plastic-window top.