Replace the u-joints on the axle shafts, that's what fixed my terrible noises. It doesn't matter if they look fine on the outside, they are old.
Reference for some help: http://www.stu-offroad.com/axle/ujoint1/u-joint-1.htm
Go spend some time around that site and keep it bookmarked, you'll learn a lot.
97 TJ, 4.7L Stroker, 4.88 Ford 8.8 w/Auburn ECTED, HP30 w/ARB Air Locker, AX-15, NP231 w/Rugged Ridge SYE, 33x10.50 BFG A/T, 4" Skyjacker, 1.25" body lift, 1" MORE motor mounts, Kilby fuel tank skid, UCF ultra-high clearance 1/4" steel skid, HMMWV-style snorkel, 63mm TB