vibration

My pregnant wife and 2 year old were leaving the mall the other day and found a flat passenger rear tire when they got back to the '9. I get the call.... Luckily there is a car dealer in the same parking lot and a Firestone shop just a bit further. She drove to the dealer who filled the tire up...

My dad's Mazda Protege vibrates when braking. No problems while accelerating and the brakes are fine. Pads and rotors. I am thinking bearings but I would suspect that it would grind or vibrate all the time or when turning but it only happens when your braking. Any ideas on where I should start...