I've had this happen to me twice.

First time with a big block Corvette - pull over, can't "see" any visible signs but its persistent decide to get the car towed to a local shop. Diagnosis ... crank is broken in half diagonally across the center main which allowed the engine to run but clunk.

Second time with an '88 Dakota. It "appears" a cap let go in the diff.

If you can drive the car then I'd discount the rear end. Just because the clunk wasn't there in neutral doesn't mean its not the engine!