I had this crop up a couple months ago. Had it tested, the alternator was "ok" but the battery was recommended for replacing. 2 months later, the whining came back. Took it to another garage who tested the alternator for a good minute and noticed the charge would be fine at first, but then drop over time, and then go up and down. So, we replaced the alternator, and its gone now.
Hopefully that fixes it for good. Only time will tell.
I have a '09 R/T 6 speed with an aftermarket Shaker intake that is functional and I have this whine every time I get on the gas and the engine comes close to red line. It doesn't sound like a "little" supercharger but a supercharger on steroids. Have had this scream for years and have never been able to figure it out.
Only things I can think of that can cause a whine like a supercharger on a stock motor running an M6 are:
1) alternator (could be bad pulley damper, if equipped, or bad bearings)
2) water pump (impeller is hitting housing at higher RPM and accessory load due to bad bearing)
3) power steering pump (if equipped)
4) AC clutch
4) Idler pulley bearing