I agree, take your car into the dealership!
Anything repaired for free at the dealer is a lot better than trying to figure out and/or repair the vehicle yourself. If the rattle in the driver's door is truly a window rattle, you might want to inform him/her of existing TSB's involving Aquapel or the BMW Gummifledge.
TSB for Convertibles / Coupes too?
Otherwise, if the dealership can't help, some members have gotten a lot of rattle control out of strips of felt placed between the door panel and the door frame. (This is a door-it-yourself {DIY} project that involves removing the door panel and placing the adhesive felt strips on the door frame, and then replacing the door panel to cushion it again the frame.) You also might want to try spraying the heck out of the door seals with 3M "Wet" Silicone Spray or lubing it with Gummifledge. They might help, but I've only gotten very temporary fix-it time from these measures.
Good luck!