I'd see if the noise is from the brake system alone or if it has something to do with the suspension being loaded. In other words, does it make the same noise if you press the brake and lift your foot, stopped, over and over again? Or does it only make the noise when you've rolled to a stop with the brakes on.
Probably the second. Which implies that something in the rear has a load on it, that is released when you let the brakes off. First thought is the top of the strut in the tower. Or a sway bar, or a control arm bushing. That's three thoughts, but they're in order.
I'd have a friend watch the rear wheels while you put the car in reverse and forward and move back and forth. Hit the brake a few times. Something will show.