I have an older model GS300 ('93). When it was about 5 years old, both front doors' exterior window frames began warping out of shape -- causing a bad seal and wind noise similar to what you describe. I took the car to my Lexus dealer, who stated that the problem was not covered by the warranty. Lo, and behold, I soon spotted another GS300 with the same problem, and wrote down it's license plate number. I went back to the dealer with this "evidence" of defective manufacturing, and was able to get both window frames replaced at a $200 set labor charge (saving about $500 in parts).
You may have the same problem -- check to see if the window frame is beginning to show signs of a bad fit to the body. If so, you may have the same problem. Good luck.