I put them in a bucket of bleach water, about 1/2 cup into a 5 gallon bucket. Let it soak for about five minutes, then gently scrub with a soft bristle toothbrush. After it's clean, dump the bleach water and fill the bucket with clean water and add a triple dose of dechlor and then soak the rock for about ten to fifteen minutes. Then throw back into the tank.
It is also good to soak your hands in the dechlor solution to clear the bleach smell off your skin. (gloves are for wussies!)