When it makes this noise while in gear, does it happen as you roll onto and off of the throttle, or does it happen while you are at a steady speed?
If it is at a steady speed, I am inclined to agree that it could be worn TC or Engine mounts, or possibly a suspension component. The TC and transmission don't tend to 'clunk' once they are under load.
Crawl under the jeep, with a helper in the cab, shift the jeep into neutral and run the TC through its gears while manually rotating the driveshafts clockwise and counter clockwise...hear your clunk?
Clutch down, transmission in 1st, TC in 2Hi, do the same procedure....hear the clunk?
You can also put the wheels in the air and check to see if your rear axle is the culprit, or have your helper load and unload the suspension while you are under it, listening for a clunk, could it be spring bushings?
Are your rear springs worn to the point that the slip yoke can push into the TC extension tower?