i love including natural local rocks in my aquarium. and ive done quite alot myself. the best method i have is a 3 step process that involves both boiling and bleach.
Step 1 put your rocks in about 2 gallons of water and add to that 5ml plain clorox bleach(about a cap full or a splash, extra beach wont hurt anything tho) make sure its fragrance free bleach. mix up the water and let set 15 min.
Step 2 rinse rocks about 20 times in warm water, i like to do this in the bathtub . after rinsedmix up in the bucket 2 gallons of water and 5ml prime or other dechlorinator. add rocks, let soak 2 hrs, stirring occasionally. with porous rocks let sit 4 hrs and change water 3 times again dosing with prime or dchl.
Step 3, Boil. get a large stainless pot or atleast with no teflon. bring rocks up to a boin covered by atleast 3 inches of water. boil at a roaring boil for 15 min minimum, i usually do an hour.(i dont recommend porous rocks for this step, for them id say heat to a simmer for 2 hrs) then let cool, remove rocks into a dechlorinator bucket again and let sit for 1 hr. you,re rocks are now perfectly clean. i recommend using hard sillica rocks such as quartz, chert, feldspar, etc for best results as they dont leach easily into water.
this method is a bit overkill but ive never had any issues with rocks after it. any bacteria will be killed and the rocks will be sparkling clean after. also if you post a picture of the rocks i can identify them for you. i was a geology student, now a chemistry major with a minor in geo. vinegar can be used in a much higher concentration but not as effective as bleach. if going for only one m ethod, id recommend boiling personally.