There are many ways in which to cleanse a crystal. Running water or sea salt in water, this you need to be careful of being some crystals do not take to water well, they tend to get gummy. Also Reg dry Sea Salt...this also..Please be careful as it will pit some crystals and gemstones. I like to use two ways.
1) Brown Rice...now this is the Safest way to cleanse...and cheapest. Take a glass bowl or dish (depending on how many crystals your cleansing) fill it high enough to cover your crystals and gems. For a 1st use allow them to sit in this rice for approx. 8 hrs. After this, when cleansing a crystal allow it to sit in the rice for about 10-20 mins.
2) An Amesthyst or Crystal Druse...allow the gemstone or crystal to sit on the druse for about 24 hrs to cleanse and recharge. After a first cleansing allow the crystal to sit on the druse for approx an hr.
There are other ways to do this like laying them in the moonlight or sunlight and allowing them to cleanse and recharge, but you need to know which stone is better charged under which light. If you charge a stone that should be charged under the moon, under the sun you will pick up a different energy not for the stone nor you, and it will program wrong.
Now onto Crystals