Our 2004 is doing something similar. In my search online, your later model is known for a problem with the radiator juice making it into the tranny. The antifreeze screws us the tranny a little and then screws it up royally. You can look for oil in the radiator and a milkiness to the trans fluid. In the meantime, the front propeller shaft is know to have issues, too. Mine started out like your and in the course of 20 miles got so bad I was afraid to drive it. It is at the transmission shop and will get a look-over on Monday.
The transmission guy and I applied the parking brake, placed it in neutral, and tried to find slop in the propeller shaft u-joints. I found a little in the front propeller shaft, but not enough to match the vibration we felt while driving. I saw on a forum that someone said it needs to be evaluated off of the vehicle. That will be the next step after the vehicle is on the rack, four wheels in the air, placed in gear with the motor running to see if the tranny is doing the vibrating. I found one guy who was told his torque converter was acting up and did a transmission flush. The flush did the trick.
Good luck! And let the Xterra world know what happened on yours!