Disconnecting driveshafts to isolate a specific diff is usually the best way for me, then roll that "free" axle on the ground by itself and listen for noise.
You can also drive it around on power with one axle disconnected since some issues are only audible under power. Take out the center rear driveshaft (to make it FWD) will let you determine whether it's the front. Take out the center front driveshaft (to make it RWD) will let you determine if it's the rear. If you hear the issue both times, it's not likely that you have two diffs that are bad so it's most likely an issue with the center diff.
Also, you should pick the truck up and spin on wheel by hand, validating the other tire on the same axle spins the opposite way and that their are no strange noises.
That's usually how i determine if the diffs are giving me issues.