Welcome to ExPo!
Ask this question in this thread. I bet you will get a lot more responses! Also throw up a picture of your 4runner! Everyone likes pictures!
Are you asking how to keep road dust from coming into the truck via the rear window? That should never happen. I've owned WAY too many Gen1 4runners - that window should be well sealed from the factory.
See if you can determine where it's coming in from. top, bottom, or sides. That will tell you where you should start looking. I know I'm missing the bottom seal that goes between the gate to the bed and I get some dust in through there.