I am quite sure that it should be done without a bra. For example, if the bra you have on doesn't fit you properly, then it may distort the shape of your boobs, give the wrong measurement, and you'll still end up with the wrong fitting bra.
Your meant to do it while wearing your best fitting bra then judge from that if need be, as in too tight go up a size, too big go down a size.

if you have perky little boobs it probably wouldn't matter but if you have any sag at all you need to measure with a non padded bra or you wont be able to measure the fullest part of your bust without having the tape too low down your back.