The inboard joint is a plunge joint and moves in and out when the tire moves up and down as when hitting bumps or impressions in the road. Seeing that you lowered the car, it may be possible that the axle is now "bottoming" against itself and causing a thump. How long has the boot been torn? It would take a while to cause enough wear in the joint to have it start clunking after the boot has been torn. It wouldn't happen right away. But as Hendosa stated, I would definitely readjust the coilovers to see if the noise went away. Also check you motor and trans mounts, if the are bad, the motor and trans will shift on acceleration and also cause a clunk and/or may cause cv axle damage.
The Auto Guru-Free Automotive Information and Advice
www.theautoguru.com