I don't see much point in boiling rocks, but it's perfectly safe to do so. I'd just give the rock a thorough scrubbing with a brush, and let it dry out at some point.
Baking some kinds of rocks when wet may cause them to explode due to expansion of water when it converts to steam, but this isn't an issue when boiling.
I think this myth is spread by people who heard about the 'don't bake rocks' bit, got confused, and thought it just applied to heat in general.
Anyways, if you have a hardwater tank, you can put pretty much whatever in it. If you are trying to keep a softwater tank, you want to avoid carbonates - rocks with carbonates (limestone, marble, dolostone, etc.) will cause the hardness to rise, and with it the pH.
Also avoid rocks with really bright colors or metallic bits - these are often due to heavy metals (copper, lead, iron, etc.) that could be a problem, but they are also pretty rare.
Try scratching the rock with a knife or nail (basically anything pointy and steel). If it won't scratch, or leaves a small metallic scrape on the rock, it's safe. If you can scratch the rock, it might be safe, but then you'll have to do an acid test (not terribly reliable) or a water soak and test.
Even if they are carbonate, you can still possibly use them in a soft water tank, but you'll have to keep up on the water changes. A lot of the fancy looking rocks people use in the ADA style aquascapes are actually weathered limestone.