Does the noise happen when only one side of your 4runner goes over a bump or pot hole, but not when both sides go over a bump? (Like driving over a speedbump) If this is the case, it could be your KDSS or a swaybar bushing.
My wife's GX470 Sport (has KDSS) clunks every time I drop the tires on one side in a pothole, or something similar, but not when both. I have tracked it down to either the rear KDSS Cylinder that may have leaked (noticeable residue on the cylinder) and lost the "KDSS Fluid" or a bad swaybar bushing, which is usually the cause of something like this, but with the additional movement of the KDSS system, I believe being low on fluid could also cause an issue like this. We were quoted $1500, by lexus, to replace the Rear KDSS cylinder, and bleed the system, so we haven't fixed it yet. With how expensive this system is to repair/work on you really should address it while it is under warranty.
Either way, you need to figure out how to reproduce it well (ideally near your dealer) then take a tech for a ride and reproduce it for them. Otherwise, they will just drive it around the lot and say they can't reproduce it. Since you are under warranty you should get it checked out incase it is something expensive like the KDSS system (Which cost $600 just to bleed!). Even if they can't find the issue, atleast you have it documented that you brought it in under warranty, and they said it was fine. Then when whatever fails out of warranty, you have something you can hold the dealer to.
You may also want to check out this thread to see if what you are experiencing is similar. At 50k miles, Lolrax's GX460 (Also has KDSS) had a rear suspension clunk that he fought for a long time. Ended up being one of the rear swaybar bushings.
Rear Suspension Rattle - Club Lexus Forums