I had this mystery squeak (squeek for those of us who can't spell) for quite some time now, I guess since I bought it in April, 2016. I knew what it was but not how to fix it. It finally started squeaking beyond just shutting the door and started squeaking on my commute and was driving me nuts so I took at look at the FSM and figured out it was likely a loose nut, but not the one behind the wheel. I only found one hit on this forum for it, so hopefully this helps someone else.
The nuts securing the hinge of the rear quarter window had come loose on the driver side. To access the nuts, you must remove the third row seat, rear mat set plate, roof headliner rear trim, quarter trim panel and upper roof side inner garnish, as well as both seat belts. I am using the FSM terms here.
Video of my squeak:
Quarter trim panel removed:
To remove:
Use #2 Phillips screw driver, remove (5) screws from rear mat set plate and pull up to remove, also remove cargo net upper mount by twisting clockwise 1/4 turn and pulling toward you, then remove screw. With 14mm socket, remove 2nd and 3rd row bottom seat belt bolts. Remove door to jack cubby, remove black push fastener (it is ribbed and a friction fit, no fancy mechanism) from jack cubby and from bottom corner, under rear mat set plate. Using T15 Torx bit (an appropriate flat blade screw driver might work in a pinch), remove trim on forward 3rd row outboard mount. Pull carpet up towards centerline of vehicle, out of the slot in the panel. Pull up sill plate on rear door. Then gently pull the panel away from the body.
Upper quarter interior panel removed:
To remove:
Use care and a sharp object to pop covers off of 3rd and 2nd row upper seat belt pivot, 14mm socket to remove the bolts. Remove roof headliner rear trim by gently pulling down, there are 5 clips holding it in, closer to the rear of the part. Remove black plastic push fastener at top corner. Remove overhead handle with #2 Phillips. Panel pulls away with a number of clips into the body and a fancy metal clip/bracket that interfaces with the side curtain air bag on the C-Pillar. That was a bit tricky.
Once everything is removed, you can now access the two nuts with a deep 10mm socket.
Top nut:
Bottom nut:
Snug them up and they should be good to go, no torque spec on these. My top nut was very loose and the bottom was not tight.
Reassembly is the reverse. It helps to have two people to align the upper trim, although it is not necessary. Seat belt bolt torque is 42Nm or 31lbf for all bolts.
Hopefully this helps someone in their quest to quiet down the beast!
The nuts securing the hinge of the rear quarter window had come loose on the driver side. To access the nuts, you must remove the third row seat, rear mat set plate, roof headliner rear trim, quarter trim panel and upper roof side inner garnish, as well as both seat belts. I am using the FSM terms here.
Video of my squeak:

Quarter trim panel removed:

To remove:
Use #2 Phillips screw driver, remove (5) screws from rear mat set plate and pull up to remove, also remove cargo net upper mount by twisting clockwise 1/4 turn and pulling toward you, then remove screw. With 14mm socket, remove 2nd and 3rd row bottom seat belt bolts. Remove door to jack cubby, remove black push fastener (it is ribbed and a friction fit, no fancy mechanism) from jack cubby and from bottom corner, under rear mat set plate. Using T15 Torx bit (an appropriate flat blade screw driver might work in a pinch), remove trim on forward 3rd row outboard mount. Pull carpet up towards centerline of vehicle, out of the slot in the panel. Pull up sill plate on rear door. Then gently pull the panel away from the body.
Upper quarter interior panel removed:

To remove:
Use care and a sharp object to pop covers off of 3rd and 2nd row upper seat belt pivot, 14mm socket to remove the bolts. Remove roof headliner rear trim by gently pulling down, there are 5 clips holding it in, closer to the rear of the part. Remove black plastic push fastener at top corner. Remove overhead handle with #2 Phillips. Panel pulls away with a number of clips into the body and a fancy metal clip/bracket that interfaces with the side curtain air bag on the C-Pillar. That was a bit tricky.
Once everything is removed, you can now access the two nuts with a deep 10mm socket.
Top nut:

Bottom nut:

Snug them up and they should be good to go, no torque spec on these. My top nut was very loose and the bottom was not tight.
Reassembly is the reverse. It helps to have two people to align the upper trim, although it is not necessary. Seat belt bolt torque is 42Nm or 31lbf for all bolts.
Hopefully this helps someone in their quest to quiet down the beast!
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