Boiling rocks won't cause them to explode.
This is a bit of a myth stemming from the warning not to bake rocks.
Anyone who has done a decent bit of camping has probably heard a similar bit about being careful what rocks you put near a fire/don't put wet rocks near a fire, etc.
This is because there is a small chance that water trapped in the rocks (either in pockets, or just interstitial pores) can convert to steam without escaping, and cause the rock to explode. And only some rocks are likely to do this - after all, a lot of primitive camping/survival skills involve both baking and boiling rocks to use as heating surfaces, to make a warm bed, to boil water in a container that can't be placed over a fire, etc.
A trapped air pocket won't explode by heating a rock to boiling tempuratures. Neither will trapped water pockets. The rock would have to be heated to well over boiling temps to generate the heat necessary to convert water to steam under enough pressure to rupture the rock. Won't happen at ~373K.
Although I don't think there is any danger to boiling rocks, I don't really see much reason for it either. Just letting the rock dry sufficiently will probably kill anything potentially dangerous on it. Or giving it a salt water soak, a dilute bleach soak, or a hydrogen peroxide soak, and then another freshwater rinse (maybe with some dechlor if you used bleach). Just don't bake it. Pouring boiling water over it could work, but I'd be concerned that the rapid temperature change might cause the rock to crack (I've done this with glass and ceramic kitchenware before).
tl;dr: Boiling is perfectly safe, baking has a small danger of exploding, and I don't think any is really necessary, just give a good soak and scrub.