I am having the same problem with all my doors (creaking when changing direction, going over bumps, etc). I was able to confirm that the creaking is NOT coming from the window frames. At first, I thought it was because I would lower the window slightly and the creaking would go away. But I now have determined that the source of the problem has nothing to do with the windows or their seals. The problem is with the doors seals only. The car has been in 5-7 times to the dealer for this problem and they have not seen this in another car. I even went so far as to have all of the seals replaced ($1,200) and it only solved the problem for a few weeks. As of today, according to my dealer and the Lexus corporate, there isn't a fix.
Here's how I cured it:
I cleaned and waxed all 4 door jams (on the actual body of the car). I then generously applied Sonus to all of the doors seals that come in contact with the car body (the seal that goes all the way around the door and the 2 other seals at the bottom). The creaking is now gone, but I fear that after repeated car washes, rain, etc., I'm going to have to be doing this every few thousand miles.
Driving the car today, I forgot how nice it was to not have the creaking - it had really ruined my view of the car and the whole driving experience. We need a permanent fix - this unacceptable.