Only way to reduce the whine from what I have read is to add baffles to the intake to reduce the air going in, but this is completely counterproductive of why you bought the charger in the first place.
Also remember that the supercharger is a hand reach from your head, while the exhaust is not. The sound from the supercharger normally be easier to hear in an NSX.
Best headers for a supercharger would be a custom set built around your motor. Large equal length(across all 6 banks) primaries , with larger secondaries and a free flowing exhaust. Cody from Lovefab makes some very good headers, but the wait time horror stories are out there for him as well. Custom parts take time, but even they have a time period before it isn't worth spending money with someone.
Edit: I thought I read the best headers for a supercharger. Exhaust would be any good free flowing exhaust. A custom one is always a good idea when you are dealing with $1000+ budget. Look for a used pride if you want something cheap and reliable.