4runner 2004 - weird noises from the back of the car

Hello,
Having my 4runner (2004, V8 limited) for almost 2 months. Since the beginning I noticed some bugging noises from the back of the car, like things are loose.
I replaced the rear shocks - nothing have been changed,
Mounted the jack + tools together (on the left panel at the boot) - the same,
Fixed the rear window (the cables was a mess but the motor works, now everything is working good - just to mention all the tailgate window mechanism is rotten..) - the car still making those disturbing noises!
In smooth roads, the noises are acceptable, but once I'm hitting bad roads the noises are worse to the point it's really bothering.
Is that normal for 2004 with 135k miles?
Thanks experts.

 

Up

 

My 2005 V6 with 150,000 miles is quiet as a mouse.

Run with the windows down. Might help find the problem.

 

Tried few times, window all the way up (closed), half way open or all the way open - something is still rattling at the back of the car. I wish this to be quite as a mouse or anything similar..

 

More ideas?

 

Have you had the hub assembly looked at? A bad bearing can make some painful nosies. My brother had to have all 4 on his 2008 Taco replaced at 75k miles about a year and a half ago.

 

Thanks expert! Actually, the rattle sounds are coming from the tailgate door, somewhere inside (pretty sure it's not coming from the bottom part of the car).
I fixed the tailgate window 2 weeks ago and the rattle reduced, but still there unfortunately.
I need to play high music so this sound will not bother me!

 

Well if you're convinced it's coming from the tailgate perhaps you could remove all the paneling from the tailgate and drive around and notice if it's considerably louder with it off. Then possibly have someone else drive the vehicle while you sit in back and see if you can pinpoint the exact location of the noise.