If the clunk only happens the first time the brakes are applied when backing up,it is just the brake pads sliding & clunking to the back of the caliper.
Mine did exactly this! Turns out the alignment shop didn't tighten the lower control arms bolts very tight. Give it a try, can't hurt.
I finally purchased a 2008 V8 Sport with 14K miles on it (with the help of everyone here) and mine does the same thing. When I come to a stop and take off there is a clunking sound in the rear. I also get a clicking/light clunking from the rear when slightly braking (ie slowly taking off in a parking lot) It only happens when slowly taking off and slowly backing into places. It drives me nuts, but as far as that I love the 4runner.