I thought I'd post here as I had this whine/whirring/winding noise from my 2007 4Runner Sport 4.0L v6. It started about 98K and of course my extended warranty ended at 100K. At the time it was a slight whirring, no big deal.
Over time it got much worse, so much that about 120K it was annoying and very hard to ignore on longer trips. The constant droning was getting to me.
Symptoms:
No change when turning, no idle noise. The noise grew with speed, but most noticeable was that the pitch would change with speed. More speed, more whine. And if you took your foot off the accelerator the pitch would change as well with deceleration. More high pitched when accelerating and a louder low pitch when decelerating or foot off the gas.
I thought it was tires first, then wheel bearings, then front axle. My VSC light would go off and on as well. Alignment was fine, tires rebalanced, no change.
After researching, I started to believe it was the front diff u-joint or front diff something. I had a garage change all the fluids in the front diff, transfer case and rear diff. That told the story.
The *rear* diff was the issue as the fluid came out gray (full of metal shavings). Not good. The sound actually sounded like it was coming from the front end, but it was the rear diff. After more research, I was pretty sure it was the rear diff pinion bearings making the noise. I took it to a reputable transmission shop and they listened to the drivetrain and agreed that it was the rear diff.
I had all 4 pinion bearings replaced in the rear diff (not cheap with labor).
That was the issue. The noise was gone and the ride was super quiet again. As a side benefit the VSC light issue went away after about 20-50 miles I'd say (can't remember exactly). I had tried the zero point calibration to no avail to clear the VSC off before taking it to the shop.
The sound was like this only mine was much louder than this example:
"4Runner whine"
4Runner whine - YouTube
I hope this helps someone. The main test was to just have the front diff, transfer case and rear diff fluids changed. This is not very expensive, is good routine maintenance anyway and it might help diagnose the issue. It also should buy you some time with the new fluids to figure out what you want to do; use your favorite garage, transmission shop or do it yourself.
I'm not a mechanic, but I would think if you let this go too long, there may be heat buildup in the rear diff and would do further damage to the rear diff gears and eventually fail the diff.
Here is a link of what the pinion bearings look like:
"2007 Toyota 4Runner rear end humming grinding noise "
2007 Toyota 4Runner rear end humming grinding noise - YouTube
My mechanic showed me the failed pinion bearing and it was much worse than this video showed. 1 of 4 pinion bearings had failed, they replaced all 4 since the diff was apart anyway, might as well.
Good Luck out there.