You don't post what year you have, but my 2003 had a problem with the rubber/plastic covering that protects the wire harness running from the back of the roof to the tailgate (electrical for lights, wiper, etc.) on the driver's side. Basically because of the design which was originally round, when the tailgate opened and closed it pulled slightly on the small rubber boot where it connects (both the body side and tailgate side), and apparently it broke the small plastic clips that held the boot flush to the metal to make a watertight seal. It looked fine to the eye, but when I pulled on the boot, you could see that the broken internal clip no longer kept it sealed. It was repaired with what I presume is the current design, which is more flat and flexes without binding/pulling on those internal clips so problem fixed--no more leaks. Before the fix, however, I was getting water in both the tailgate and also inside the body where the water was running down the raar sides and would exit through those tiny backing mirrors in the rear columns.
If not the weather stripping, check that wire harness rubber/plastic boot and make sure you gently pull at it to make sure it is sealing against the metal properly.