Update: Just got a call from the dealership, and they are going to order a new drive line. The service adviser said that this is a quite common issue with certain Toyota's. He said this occurs because as the nose dives (hard brake) and the back end rises, the drive line and the slip yoke become misaligned and when the vehicle returns to a level position (once stopped), the yoke slips back into its original position, and that is what produces this "clunk/thunk" or "bump from behind" sensation.
Hopefully, the new drive line will fix the issue, but the adviser said I could be back before my 60,000 warranty is up for another one. I hope not. I will update you guys when I have the new drive line installed.