I have a 2013 x3 as well, January-ish build of 2013. I have the whistle too, passenger side, usually over 40-50MPH. Just brought it in, they failed to fix it... I think it's now worse because they made the cabin quieter by replacing door trim and tightening the passenger door. I think it's coming from a molding or mirror, or roof rail... I drove at speed and lowered the window and still heard the noise.
The masking tape idea is an interesting one. I'm scheduled to take it back in, in a few days. Maybe I'll try that.
Did you get it fixed?