Every car is different, but my door rattles were coming from the latches themselves.
A temporary fix was just putting a few layers of masking tape on the flat, mating surfaces to confirm that's where the noise was coming from.
Seven years later, I haven't been moved to find a more permanent fix, so I renew the tape every few months or so.
My old BMW 2002 had a similar latch that never creaked, but what is hard plastic (or ?) on my Speedster was a more pliable nylon on the 2002, so I'm guessing finding better material for that piece is the right fix.
At any rate, some tape will tell you if that's the source of the noise on your car.