I boiled water, turned the heat off, and dropped the rocks in and let them stay in there until the water cooled. (A LONG TIME.) Then I let them air dry, and I scrubbed them off with warm (as hot as I could tolerate it) water.
Boiling water nearly kills everything... Be careful though, rocks from outside can greatly increase your water hardness! (Meaning gross water rings.)
Do not use soap or cleaner on them, rocks absorb things and whatever you pour on it is not going to come out unless with a deep soaking.