I have the 2005, so I am assuming that the wiring is the same. When I asked this same question, here is the answer I got from the forum, which checked out right when I called Tekonsha and asked them--don't know if different brake controllers have different wiring?
OK:
Prodigy color -> 4 runner adapter harness color
black to black (battery +)
red to green/yellow (brake light)
white to white/black (ground)
blue to yellow (brake light)
The 5th wire (green) in the 4runner harness is unused (tail light). Just cut it short and insulate the end.