My 99 SR5 has a noise that just started coming from the trans area. Noise is there while in gear or in neutral, but only while driving. At idle it goes away.
I uploaded a video of the noise below:
You mentioned only while driving but not at idle. Is there a certain RPM at which it begins? In gear but off the gas does it continue? See if you can play with different driving patterns and gear selections (AWD, RWD, 4WD, Drive, 2, 1, Center Diff Lock) to create changes and use that to narrow down the origin. If it is replicated in Neutral without moving, have a friend keep it above idle while you go underneath to determine if it is from the tranny or TC.
I am guessing so could be some thing else. Only while moving makes me lean towards the rear differential whine or double cardan joint going out. Is your maintenance up to date? vis à vis when were the atf, both diff and transfer case. Changing fluids and greasing joints wouldn't hurt. If your rear differential is going out 75w140 might buy you some time.