let me start with saying this fixed my problem and i have no idea if it will fix yours.
i to had a big problem with alt whine. i hooked up alot of cooling fans for a box that i built over the amps so i could have some cargo space in my suburban. once the fans had been hooked up i got a horrible whine. i solved my problem with running the amp activation wire from the head unit into a relay power directly off of the batteries for the amps and the whine completely went away. not saying this will fix your problem but for a $5 relay and about $5 worth of wire and maybe 20min of work its worth attempting imo.