The orginial bumper-to-bumper warranty on the car (3/36) covers all parts except those subject to normal wear and replacement (brake pads, wiper blades etc). The top is not considered 'normal wear' according to the warranty.
However, I think you guys are talking about extended warranty and if that is the case, all bets are off. Extended warranties are basically a bait and switch and they will try to find a way to NOT cover whatever it is you are claiming.
I would bail on the dealer if I were you (get it fixed 'one way or another' wtf does that mean?) We'll fix it and you pay for it... that's one way
You can search for glass window replacement at
www.s2ki.com There is a photo-illustrated thread for step-by-step how to put a glass window top on a car that originally had the plastic window. It takes a weekend, requires drilling a few small holes in the top frame (aluminum, no rust) and some riveting (parts available at Home Depot). The top can be purchased form
www.hardtopguy.com for about 700 bucks. Your car will look like new.