I found the rattle comming from my roof rack. The two screws holding the crossbar to the track member was loose. After tightening the two torx screws I have no more rattles in the 4Runner.
I thought the noise was coming from the front driver side or the cargo area, but it was the roof rack.
I just purchased a 2007 v6 SR5 with 38K miles on it and when I drive 60+ miles per hour I also get an intermittent noise comming from the drivers side of the car. It's not a loud noise, but it's noticable even with the radio on.
Let me know what you find out.