Sorry to revive an ancient thread here, but I figured I'd share my knowledge here.
The issue may not be greasing or lubricating any bearings, or have anything to do with the brake lines. My 4th gen limited 4runner had an endless clunking noise when I stopped or accelerated, more pronounced when I changed acceleration quickly, but it still happened on slower stops, especially on a hill.
Eventually, I figured out it was coming from the tire jack in the back left side of the trunk. I bought mine used, so I'm not sure how snugly it fit from the factory, but there was enough room for mine to move around, a bit up/down, and a bit forward/backward. I just stuffed an old wash rag around it, and like magic, no more clunking sound.