Try this, set the HU to play just one side of the audio system, say the drivers side.
Crank the tunes, CD, and listen for a passage in the music that produce's the problem.
Put your hand on the door panel during that passage and see if there is excessive vibration and with hand pressure applied, does the problem go away.
If so, add some acoustic padding inside to door to see if the vibration can be dampened.
Also look for anything that may be loose in there, wires etc. Tie wrap those down.