If the window is clunking on the way down, it could be from the well known bolt backing out problem. Check the GM recall site to see if there is an outstanding recall on your VIN for this (it was issued years ago so it may have already been taken care of.)
See here for a thread on correcting: viewtopic.php?t=19269
Also, solid advice above regarding the window weatherstripping as these tend to deform considerably over time. I replaced the fronts which were in considerable disrepair and it made a noticeable improvement on how tight the windows fit (not to mention a huge decrease in wind noise.) That said, the windows had a lot of play in them even when these cars were new so do not expect perfection.
03 Vibe base. Born 10/14/2002 06:07 AM
Neptune. Auto, Moon & Tunes, power package. 130k mi.
'13 Sonic LT - 1.4L ECOTEC turbo/6A. 88k mi.
'15 Escape SE - 1.6L EcoBoost, FWD. 42k mi. (hers)