Ahhh, the infamous drive line "clunk". Do some searches on this board and you will find plenty of info around it.
I started noticing the "clunk" when my brand new runner had about 2k miles on it. After doing some research here, I've been greasing the drive shafts every 5k when I change my oil. Haven't had a problem since.
http://www.toyota-4runner.org/showth...threadid=28414
If it makes you and others feel any better about it, I had the same problem only worse on my old '00 Grand Cherokee with full-time 4x4. I'm not making excuses for Toyota, but other manufactures are not immune to this problem either.