When was the last time the water pump was changed? I know you have not had the 4runner very long but if the person that owned it before you, replaced the head gasket and not the water pump, that might be the issue. Everyone is right to look for leaks first, because if your cooling system cannot develop a good vacuum, your coolent flow will suffer. Start simple, radiator cap, Leaks, and last item would be the water pump.
