My Safari's rear window is the emergency exit. If this is the one you are having problems with, make sure to keep it operable!
If it is this window you are having problems with, I think the dealer is probably saying to replace the rubber seals around the glass. I would agree with this.
I have had leaks at this window. Keeping the weeps clear/open is very important. I have not been successful at completely eliminating water intrusion at this window, but what leaks in also leaks out the weeps immediately. This window is so large that condensation is a problem during cold weather. I have had drips come off of it when there was no rain.
2014 Silverado 1500 5.3L maximum trailering package (yes, I'm towing the 34')