I had this same problem in my 2010 4runner when I purchased it new in late 2009. I had the ECU re-flashed per a TSB about 9-12 months later and have never noticed it again.
I also had the drive-line BANG when stopping at intersections or after releasing my foot from the brake.
They replaced the entire drive shaft per a TSB under the drivetrain warranty about two weeks ago and this problem too disappeared.
Which dealer did you take it to may I ask? I have the same thing and a couple of minor items that has a TSB on it, bit the dealer or tech refuse to do anything. All they say is it not there when we test drive it. My 4 runner has 30k on the clock also a 2010 Limited. By the way, its the seat clicking when I brake. It drives me nuts to have that little cracking going on back there.