2001 325i 5mt. 2009 535xi Touring 6mt.
Good job isolating it from different gears, as you say it must be somewhere in either the driveshaft or differential. I would checkout out that center support bearing on the driveshaft. I recognize it is annoying to get to, but such is life. Perhaps it would be easier for you to jack the rear end up, disconnect the driveshaft from the differential, put the transmission in neutral and see how the driveshaft feels as you turn it by hand. At the same time while it is disconnected, you could spin your wheels by hand and see if there is friction. Your hands will never supply as much torque as the engine so it's possible this won't help, but I think you'll be able to identify a bad bearing.