Amethyst and hematite can both be cleansed in water. Im unsure of the isis crystal as Im not sure of the physical makeup of it. An example of a crystal you dont want to submerge in water is Selenite.. But i have found that using moonlight to cleanse these works wonders, as does earth.
I, personally, have a strong affiliation with the sun, so alot of my crystals are cleansed via sunlight. For The ones that discolour in sunlight I use salted water.