Your problem sounds like disk brakes unevenly worn. I have had this problem before, and this is one of the most common causes of vibration when touching the brakes. I would have the front disk brakes rectified.
Hope this helps.
Dear 4Runner owners: I had my 5th Gen 4Runner (2011) armored. Everything ok, except the rear wiper will not work. We all know that the wiper motor needs a window-all-the-way-up signal in order to function. In my case the window mechanism was dismanteled. Now, still connected, I have the window...