from what i've gathered by speaking to multiple installers, the labor is the same whether you fix the vinyl window or install a new top. either way, they have to remove it, and put it back on. so most installer have recommended just getting a new one.
i looked at autotopsdirect.com. seems to have good rep and cheapest prices. new top about $600 with glass window.
now i have also run across this.
http://cgi.ebay.com/ebaymotors/ws/eBayISAPI.dll?ViewItem&item=270741161017&ssPageName=ADME:X:SCO:MOTORS:1123
not sure if this is "too good to be true". glass top for only $370? thoughts anyone?