Edit: this was done on a 2008 GX470
So after reading a ton of different posts including this thread i finally figured out how to get to the nut/bolt that pushes the rear quarter window out enough to get at the clip that holds down the weather moulding. I went the route of completely removing the lower interior panel in order to get under the top half of the panel where the nut is hiding.
Followed these instructions for safe removal of the lower interior panel:
Adding Dynamat behind subwoofer - ClubLexus - Lexus Forum Discussion
After that was off the top portion just pops out along the locations where is snaps in. Didn't take it completely off, just the area around the Seat Belt.
One thing to note of course is that if you do this - when you're closing it back up again make sure that the plastic seatbelt adjuster on the outside matches up with the mechanism underneath or you might break it.
Once that was clear I was able to find the hole with the nut in it:
Here is that hole from a better angle, you can see there is a pin in it that keeps the nut from falling inside into a black hole
You'll need a long socket to be able to loosen the nut and clear the bolt, or you can fake it and invent your own tools like i did taping the socket to a pair of pliers:
Once that's loose - like everyone else said, you can get to the clip and rip that old crusty moulding off there and replace it. I did also create another tool to remove the clip without destroying it - i connected a small screw to a small screwdriver with some wire to be able to push the button on the clip and extract it as clean as possible.
Probably did more than i needed to, but popping out all the panels gave me way more flexibility with accessing the hole that the nut is hiding in.
thanks for all the info here guys, just wanted to share my experience as well and give back.