Sounds like you may have worn out upper control arm bushings, braking action repositions the load on the "A" arm when brakes are applied and usually causes a heavy clunking sound, pump the brake pedal continues the sound in sucession to the pedal pumps.

I have a car I just bought and notice this same thing the minute it came off the car carrier and I hit the brakes, previous owner forgot to tell me the upper control arm bushings were shot!

Check all your ball joints and tie rod ends and any linkage while you're at it for signs of wear.

Good luck