Check with your insurance, and avoid using the words "wear & tear". You were operating the top normally, so simply explain that the window cracked while the top was in motion. There's no guarantee that they'll cover it, but it can't hurt to try.
The short answer about glass is that you can't do it on a plastic-window top. If you look at any aftermarket tops with glass, the window is much shorter in height than the plastic, and this is to allow the top to fold. If the glass were as large as the orignal vinyl window it would either crack from trying to be bent in half or it would rip itself out of the top. The smaller window does take getting used to, but if you're not a tall person it won't be too much of a problem, and it's a non-issue when the top is down.
You
can replace your top with one from 2003-2004 Boxster. I'm assuming that your car is older than this since Boxsters were using glass from 2003 onwards. Anyways, in order to use the 03/04 glass window top, it requires replacing the actual frame of the top as well. The vinyl window cars have a 3-rib top frame, while from 2003 onward the cars used a 4-rib frame, and that additional rib is what allows the top to fold properly even with a glass window that is nearly the same size as the old vinyl window. There is more potential work that has to go into this option though, since the top may not cycle properly due to other components from the 3-rib design era.
People have stitched in new windows before and seem to have had some success, either doing it themselves or having a shop do it for them. The cost can vary based on that, and I can't speak on the effectiveness of the job and the watertightness of it. Some shops will refuse to do this without removing the top from the car, which will incur labor charges, and some will refuse to do it at all because they don't believe the top can be re-sealed properly after the new window is stitched in...and some probably just want to make the money from selling you a new top. You could avoid the labor charges by taking the top off and putting it back on yourself, but that's a choice for you to make.
I'm sure others will chime in here with their experiences and advice. I had a similar thing happen to me earlier this year, though the window seemed to simply crack from the temperature drop, and I decided to replace it with a new top with a glass window. The original top wasn't in awful shape, but it was 14 years old and could use a change. You could see if there are any upholstery shops, and automotive ones in particular, in your area (Redan is one here in CT, not sure if they're in NY). Once you get a quote from oneor two of them then you can evaluate what is most cost effective for you.