Here's my service history for a "whistling" (mine was more of a growl) sound from the intake plenum on a 2002 3.0:

1st time: Installed foam donut absorbers on two metal lines that run near the firewall (didn't work).
2nd vist: Oil Service (did quiet the engine somewhat but still didnt work)
3rd: The BMW senior engineer suggested, replace belt and belt tensioner (helped somewhat but still an ocassion whistle)
4th visit: Tighten the pleunum and cleaned intake (again failed)
5 visit: Insisted they change the idle adjustor module as suggested here. Sound appears to be gone or I just gotten used to it.

Start with the idle adjustor; demand that the dealer replace that part. If that fails, try the belt & tensioner.