Wash lots, then sterilize by:
heat - put in oven, in BBQ, hot sun, etc.
bleach - I soaked mine in 10:1 bleach, then washed the heck afterwards, finally rinsed with a good dose of dechlorinator. And then I left the rocks out in the sun for a week just in case so any remaining bleach can break down / dissipate. <The last step is just for me being paranoid!>
salt - strong salt solution will kill most bugs, although I hadn't tried that myself.