Funny, you are kind of describing a similar noise I have with my 08 v6. Did you say the whine seems to get louder as the engine warms up?
During acceleration there is no whine but during deceleration, e.g. when you take your foot off the gas and the rpm’s start to drop does the whine become noticeable?
Does it seem to be most noticeable right around 1500rpm?
Can you hear the whine in the background while driving when the rpm’s are near 1500rmp or so?
I posted a thread a while back asking about a whine noise I was getting:
http://www.toyota-4runner.org/general-discussions/66093-v6-4runner-engine-whine.html
If you forget about the fact that I installed an oil cooler, I would be curious to know if the description I gave of my whine is the same as your’s?