My 2002 Dakota 4x4 5 spd has developed an intermittent high pitched whine when travelling at highway speeds. It sounds like it's coming from just underneath the cab. I've done some research and found out it could be the pinion bearing at the rear diff. The only thing is when it starts to whine I put the clutch to the floor and the whine goes away instantly. Does using the clutch affect the diff or am I looking at a more severe and costly problem?
Any help would be appreciated.

Maybe a throw out bearing about to head south

I too would check the throw out bearing. The noise going away when you step on the clutch leads to transmission, not pinion. Does this occur under load or coasting with the clutch out.