I also have the noise on all my four doors.i think it comes from the control panel cover.just press it and you will hear the noise.i started hearing this the week after i got the truck.i brought it to the dealer to see if they can atleast tighten it.but then they told me that they are tight enough.problem with 5th gen is its made out of alot of plastic.and the location of this control panel should not be attached on the inside door handle.thats why when you try closing the door from the inside you will hear this creaking noise.dealer also showed me brand new 4runners which have never been driven,same thing,door panel cover cover also make alot of noise.so i guess there is nothing we can do.