Immersion in boiling water for a few seconds is a lot less effective against bacteria, than people think, you'll need more time in the boiling water than just a minute or two to kill everything. My suggestion would be to mix up a bleach solution(1:10 dilution) and soak the rocks. Put the rocks in an empty 5 gallon bucket as full as you can get it, then pour in premixed bleach dilution to cover the rocks, wait a half hour, pull out the rocks, rinse them off and let them air dry for a day. and repeat for as many rocks as you need.
(the following is from wikipedia concerning sterilization).
Boiling in water for fifteen minutes will kill most vegetative bacteria and inactivate viruses, but boiling is ineffective against prions and many bacterial and fungal spores; therefore boiling is unsuitable for sterilization. However, since boiling does kill most vegetative microbes and viruses, it is useful for reducing viable levels if no better method is available. Boiling is a simple process, and is an option available to most people, requiring only water, enough heat, and a container that can withstand the heat; however, boiling can be hazardous and cumbersome.
Bleach
Chlorine bleach is another accepted liquid sterilizing agent. Household bleach consists of 5.25% sodium hypochlorite. It is usually diluted to 1/10 immediately before use; however to kill Mycobacterium tuberculosis it should be diluted only 1/5, and 1/2.5 (1 part bleach and 1.5 parts water) to inactivate prions. The dilution factor must take into account the volume of any liquid waste that it is being used to sterilize.[24] Bleach will kill many organisms immediately, but for full sterilization it should be allowed to react for 20 minutes. Bleach will kill many, but not all spores. It is also highly corrosive.
Bleach decomposes over time when exposed to air, so fresh solutions should be made daily.[25]
