What makes my 4Runner ride so rough on the rear end.

Stock suspension and tires? check springs and shocks.

I'm late to the party on this one but I will throw in my 2-cents for others who might have this same issue. More than likely one of your bushings on the top of your rear shock OR a bad shock. I just had this issue about 4 months ago where just pulling out my driveway onto the street with that little 1 1/2" drop would make the back of my 4Runner sound like it was falling apart. The bushing was gone. replaced it for $3 and i was good to go.