I voted "No", because the thud doesn't happen when I brake hard... it happens after I release the brakes after harder braking.
2006 V6 with 80k miles. I last lubed the slip yoke on my driveshaft about 5k miles ago and it's back. This Spring, I think that I'll pull the driveshaft apart, clean it up, and reapply some super slippery stuff.
My '98 Tacoma did the same thing brand new from the dealer floor and the Service Techs told me that it was the transmission "torquing up" against the rubber mounts during a stop. It will stay torqued until you let off of the brake and allow it to "drop back into place".
It could be the same condition on the 4Runners, but keeping the driveshaft lubed definitely helps.