My passenger side door speaker is not working right. When I close the door the speaker does not work, but when I open the door it works and plays just fine. This is an aftermarket speaker but I had this problem with the speaker that came with it. None of the wires are bare so it can not ground out and everything seems to look all right with the wiring. I have no idea what the problem could be and any help would be appreciated.

The wires don't have to be bare to have an intermittent open circuit like you've described.
Somewhere there is too much flexing of the wire leading to that speaker and it has broken. Now it will only get worse.
You could search for that partial break but it would be easier to simply run new wiring to that speaker and remove the old wiring and throw it away.

It's likely an internal wire break, which commonly happens when bundled tailgate wires break inside the insulation due to constant flexing. It's the same situation you are facing. With an ohm meter and T-Pins, you could locate the break. Ensure your replacement wire is stranded.