Does anyone have problems with the spare tire making a clunking sound over bumps? I think that is what it is? I can't see anything else that could cause it in the suspension. Any help would be appreciated. I think the whole arm that holds it is loose.

What year is your ML?

The ML's have lots of suspension things that cause creaks and clunks back there. Some primary suspects are Shocks, bushings, torsion bars. search for "clunk or creak in suspension"

It could even be the rear hatch not adjusted tightly.

I think I found the source of the noise, the rear seat. I was vacuming the interior yesterday and hit the back seat with my arm and it made the sound I hear when driving. So I folded the seat in th back down and my wife says it is quieter. i have not yet drove the rig yet but I will let you all know.