Proper driveshaft lubrication or balancing?
Please note that I do not have the mechanical expertise of many of the contributors to this board, so take my comments accordingly. Furthermore, I drive a 2000 SR5 V6 with a 5 spd manual, so my experience might not even apply to your 4th gen rig, but it could be worth considering. I purchased my Runner from the original owner who kept all service records. The records showed oil changes, including lubrication of the drivetrain, every 3000-3500 miles, which is one reason I decided to buy the rig regardless of the high mileage--108k. Also, all Toyota prescribed maintenance and most of the oil changes/lubrication were done at a Toyota dealership. Sounds good so far, right? Well, my T4R had an interesting chirp/ whine when I let up on the gas, so I took it to an independent garage where a trusted mechanic found that all the drivetrain lubrication points were bone dry. He lubed'em up and the noise soon disappeared. He told me that lubing is normally not needed every oil change, so mechanics get in a hurry and don't always check all the points, figuring it'll get done next time anyhow, and that'll be soon enough even if they're almost dry. So, is it possible the vibration could be related to neglected lubrication of the drive-shaft and U-joints? All of the T4R's above are 04 and 05's. They must have had several oil changes including PRESUMED lubrications by now.
2. Also consider this: Did you know that the driveshaft or your brand new unit wasn't produced perfectly balanced? It must be spun and balanced at the factory just like your wheels/tires? I didn't know this until I had to nurse an off-roading '95 Tacoma with 156k on it. You can see the balancing weights if you inspect your driveshaft. One set of weights on my 2000 T4R are just in front of the U-joint near the center of the rig. Could your driveshaft be out of balance? I wonder about this because you report the vibration is more pronounced at certain rpm's, and we all know that vibration at certain rpm's is a characteristic of a wheel/tire that is out of balance. Maybe the factory driveshaft-balancer was out of specs for a certain production period. This is a remote possibility that the service manager will not want to entertain, I'm sure.
3. Or, if it turns out to be true that "they all do it," and you prove to yourself that nothing is defective, maybe you just need to accept and celebrate the fact that your rig has an off-roading heritage, and its okay if it feels a little bit more like a truck than you expected. Good luck. Keep us informed.