The CLUNK is from trapped air in the driveshaft. When braking occurs the rear-end twists a bit extending the driveshaft. When you finally stop, the rear-end is cocked and ready to unload and force the driveshaft back together. When it finally overcomes the air trapped in the driveshaft it lets go with a pop! My 05 GX470 was dealer repaired including the new driveshaft as well as sturdier rear lower controlarms (to lessen the rear-end flex). No problems since. A local mechanic had his own fix for his wifes GX. He drilled a pinhole in the driveshaft to let the air escape thus fixxing his "clunk".
