Take the car to a trim shop that does replacements on convertible windows. They can usually replace just the window... price varies. I've read forum posts of $200 to $500.
A new, German-made top from Ebay is $400 plus a hard day's work to install it yourself. My mechanic quoted $400 to install one if I brought the top to him.
You do not want to even talk to the dealer as their prices for tops begin with a four digit price and go up from there.
This may well be the perfect time to save up and buy the newer glass window replacement tops for non-glass window boxsters hitting the market for about $1100.00. I know you probably didn't want to hear that price tag... I winced when I heard it as well—but it will certainly come down over time.
Hope this helps.