Well if you get the vibration at the same highway speed regardless of whether you are in 4th, 3rd or 2nd (will it even go that fast in 2nd) then it is something between the transmission output shaft and the wheels.

If you get vibration at different speeds in different gears but same engine rpm it is something between the engine and transmission input shaft.

I can hear my diff growling when I have the truck in the air and its in gear. This is not exactly the same test as having the wheels on the ground, because the only load on the driveline is the wheels spinning freely in the air. I still think it's a useful test. You need someone in the drivers seat though.