Sounds like the classic drive shaft clunk, I'm surprised that more Toyota dealerships don't know more about this. There was a TSB for the same problem with the Lexus SUV's. Us 4Runner owners got the shaft (nice pun there). Pretty easy fix if you're willing to get under your 4Runner. Plenty of pictures and discussion here:
http://www.toyota-4runner.org/mainte...ting-pics.html