Sorry about my english but I will try to help you.
The electronic card that control the rear windows is in the interior of the rear fender driver's side ( in my 1993 4runner ).
There are little relay that control the up and down window action. You can check if everything seems to be ok.
You can also open the cover of the tailgate by the inside or the truck. You will see the window motor and if you can, unplug the two motor wire and put a 12vdc power supply on it to see if the motor is ok. Switch the polarity on the motor to simulate a up and down action.
If nothing work, the motor is probably dead. If it work, maybe you have a burned relay on the electronic card.
You can also verify this below because if your window stop in the middle of his action, maybe its a bad limit switch that block the windows.
You can also check if the button up/down inside the truck work well and if the key switch on the tailgate is ok.
There are some kind of "safety" that lock the action of the window. You have to check if your rear wiper is at its place because there is a kind of limit switch on it to block the down position when the wiper is in action.
There is also a limit switch inside the tailgate. You have to open the cover by the inside of the truck and see if the limit switch work correctly ( it is near the windows motor ).
There are also another safety that lock the window, there are limit switch each side of the tailgate where you have a kind of hook that keep the tailgate close.
Don't let Toyota change the electronic card because it cost approx 400$ !!!. In many case, it is just a defective relay that you can buy at radio shack for 3$.
Let me know if it help