It could be the center diff bearings. I had a 2003 5 speed that whined while accelerating. Holding a steady speed made it quieter, and engine braking made it go away completely. Accelerating/decelerating changes the direction of thrust in the transfer gears. In my case, one bearing was good, the other was on the way out.
The sound seemed to be coming from the shifter area. The best comparison I heard someone say in a forum was that it "sounded like a spaceship". :biggrin: