I actually went through this recently. I even had my friend drive my 4runner while I was in the cargo area trying to press on panels, etc. I could not find the squeak but I knew it was coming from the tailgate somewhere. This squeak was strange as I got a squeak when I was going slowly on my driveway flexing the suspension. But going over big bumps no squeak at all. Smaller bumps I got the squeak.
Fast forward 2 weeks and all of a sudden my tailgate started to unlatch while I was driving. I pulled over closed the tailgate, closed fine. Once started to drive it opened again. Then one day I had no problems at all with it. I ordered the tail gate lock motor anyway since I go on many overland expedition type trips and I did not want the tailgate lock motor to act up during one of these road trips.
Changed the tail gate lock motor and switch while I was at it.
Squeak is gone!
What I suspect is that the motor was not having the tailgate lock fully which did not press against the weather seal tight even causing a squeak.