1995 Mazda MX-3 thumping noise

1995 Mazda MX-3 mileage: 146,000. I recently noticed the outer CV boots on my car were torn on both sides and I had them replaced. I noticed they took the CV axle out to replace the boots. The problem is that when I step on the brake and the car is about to stop it makes a repeating thumping noise coming from the CV axle area. I checked the brakes and they were fine and I had a mechanic check it out, he drove the car and inspected and he said he heard the noise but he could not tell what it was. He said his van makes the same noise, well that didn't help much. What do you think it is? Thank you very much for your time.