clutch pushed in = no noise?
If the tranny gear is not engaged, then the drive shaft is not under load. The U joints usually make noise while under load when they are bad or going bad. That would explain why you can't hear the noise when you press the clutch in. Crawl under the jeep and shake the drive shaft. If there is any play at all the U joints are bad.
89 YJ, 4.2L MC2100 carb conversion, nutter bypass, AX-15 tranny conversion, rhino lined tub, 33" Treadwright Mud, 2.5" RC lift, 4.10 gears, Aussie locker front and back