I had this same issue a while back and it had nothing to do with the breaks rather the triple tree stem upper nut was loose, so each time I laid on the breaks the front felt like it would rattle. So I assumed it was the brakes but in my search I loosened the stem nut and retightened it and the problem went away.
Worth a try.
Other wise I would say to loosen up the entire brake system and tighten properly to make sure each piece is torqued properly.
If that fails you may have a warped rotor even though it looks straight it takes very little to give a vibration.