I'm only guessing but I suspect it has to do with a gap somewhere between the windshield and the windshield surround moldings . . . Do you know if the windshield has ever been replaced?? Take some plumbers putty (or something similar . . . Play Dough? or just 2" wide tape) and pack / seal around that whole area. Drive the car and see if that stops the whistle.

Opps . . . I just re-read your post and see that there is no whistle when the top is down. Probably not what I thought . . .