I used a wire brush when I cleaned rocks for my tank, one that you would use for a grill. I also put them in boiling water to kill anything that was lingering on them.
Make sure they don't have limestone in them if you have PH sensitive fishies! Rocks with limestone in them will cause your PH level to go up
If i remember correctly, if u put a few drops of white vinegar on them, it will bubble if it has limestone present. When I did it, I just filled a whole bucket up and put the rocks in one by one Vinegar is cheap lol.