It's usually not the window area leaking, cause they go up into the frame. The culprit is either the weatherstriping or your door is misaligned. The door thing sounds far fetched but that is the problem I had. I had to raise the door hinges on the body to fix the leak. Somebody at one time had to have had this door off.
i have the same problem.. im gonna replace all the weather stripping and see if that helps it.. i hope it does cause the wind coming inside the car gets really loud at about 60 mph and i cant stand it