If it only does it when you're applying the brakes, then it's almost certainly the rotors needing to be turned. This could be just because of normal wear (I don't know how long you've had the rotors) or because you ran through a puddle while the rotors were hot,etc.
Alignment doesn't really cause vibrations. It can cause tire wear that could result in vibrations, but it would be felt at other times than just braking.
