When purchasing your crystals its best if you don't know to ask if they can be put in salt water. Some like selenite and turquoise are very soft and porous and need to be wiped down with a soft cloth and an alternative to clear them energetically, is to lay them out on some rice. Then throw the rice away. I find i like to leave them overnight to clear on the rice.
For the the stones that you can wash I make a salt water bath in the sink . Make sure you rinse them well to get the salt off the stones or on some it can cause dulling.
Or rinse them under water, but I don't find this feels as clean.
Sometimes there is confusion around what actually cleans and charges crystals. As a "dusting" in between a big clean of my crystals I will use sage, or palo santo smoke. Light either one and use your feather or blow the smoke onto your crystals and ask that they be cleared of low energies build up.
You may also use Reiki symbols for clearing and charging, or draw your own sigil over the crystals. (see magical arts forum for more info on sigil work)
You can charge (not clear) crystals by placing them in a spot where they will receive direct sunlight or moonlight. I wash my crystals on or just before the full moon and leave them outside (or in area that will get the light) for 3 days. The strongest energy of the full moon is find is the 2-3 day build up to the moon and a day or 2 after.