How do you work on a rear window of 1990 Toyota 4 runner when the motor stopped with window up?

The best way, is to go inside, remove the tailgate's interior trim and moulding. After removing the plastic sheeting, you can then access the regulator (the scissor looking part with the motor). Remove the bolts that hold the regulator. Now very carefully without bending in or out, because you could break the back-light (rear glass), lower the whole assembly down into the tailgate. You may have to jiggle it up and down slightly. When the glass has cleared the frame, pull on the cables that activate the latches. With the help of an assistant on the outside lower the tailgate. Now you can work on the problem with ease. Inspect the regulator, wiring etc. for wear and tear as well as rust.

Good luck!