I just wanted to share this because I have seen a few posts on here stating similar issues....
I have an '06 Reg Cab manual. I noticed a noise getting progressively worse the more I drive it. It sounded like a grinding noise or vibration coming from the transmission area.
To try and isolate the problem I removed my foot from the accelerator. That is when the problem happened. I only seemed to hear it on the highway above about 65 MPH. So that means I was usually in 5th gear, so I decided to see if I heard it in 4th gear so see if it was the gear in the transmission.
The problem still persisted. So I tried listening for it around town in the rest of the gears, but I heard nothing. So that lead me to believe the transmission was probably okay and it was something else that would spin when the truck was moving.
Then I read on hear somewhere the someone have bad bearings or something on the input shaft to the drive shaft. So that made sense to me, when the engine is under load on the highway, the RPM and vibration would be just right so I would hear the noise.
I took it to Toyota and had them look at it, and I told them my theory. They called the next day and said my drive shaft was broken and they were going to replace it. So if it had a crack in it, or it was unbalanced or what I do not know but now the truck runs perfect and no more noise.
If the drive shaft was unbalanced I am no mechanic but I am pretty sure they could just re-balance it, but that is just my thought...Anyways I have only had the truck back for about a day but I have done a bunch of highway driving since I have had it back.
I will keep you posted if the noise comes back, and I hope this helps someone else having similar issues.