There are many ways to clean crystals of negative energy. Here are some suggestions:
Outside Method: Place in Sunlight (See Sunlight chart below), Moonlight or Rain (See Water Method) for up to a day. Placing the stone on or near a plant often quickens the process.
Crystal Method: If small, can place on a Quartz or Amethyst cluster. Great way to clean necklaces. Clusters could be dedicated for this purpose with a clear intent. Clean Cluster every month or two in rain or sunlight if possible. An amethyst geode works great for this purpose.
Sage Tea Method: This method is effective with less possibility of damaging the stones. Take a sage (fresh is always better but not mandatory) and brew a pot of light tea and allow it to cool. Place your crystals in a bowl (use a glass bowl) and pour the cooled tea over them. Leave them overnight. Then remove them and rinse with clean and pure water. Since they are chemicals in most water systems you may wish to buy a gallon of distilled water for this purpose.
Smudge method: Pas stones through the smoke of scented incense such as sweetgrass, frankincense, sage or Dragon Blood of passing them through a candle flame.
Water Method: Place stones under alternating hot and cold running water for 5 minutes (or in rain for many hours. It is preferable to have water filter system on your tap to filter out some of the chemicals if possible. This is quick and easy but the drawbacks; some stones lose their coatings when they get wet such as Lapis, Malachite, and Sodalite. They often are stronger after this is done, though, but they get damaged faster. Cleaning these stones in the sun and moonlight works fine. Stones really like rain. It cleans them much better then the sink method if the weather is conducive.
Sea Salt Method: Use about 1 cup of sea salt to 2 cups of natural spring water, or distilled water. Place stones in the salt and let them soak for the better part of the day, or overnight. If the day is sunny, let them dry in the sunshine for a few hours, or if they are lunar stones, lay in the moonlight on a window sill through the night.
Sand Method: When all else fails, or you are having a hard time cleaning something, bury it in the moist sand (or soil).
Mantra Method: Hold stone with your right hand and chant a mantra. Om Ah Hum or Om Mani Padme Hum. I use the Mantra of Light of the Buddha Mahavairocana. Before chanting form an intention to cleanse the stones.
White Light Method: Hold the stone in your right hand and visualize a beam of pure white light descending from above on to the stone. Hold your attention for as long as you can, though I take about a minute to clean it using this method. This is a very good method of training to bring down the white light for healing and protective method. Can also use in conjunction with mantra chanting method.
Solar Plexus Method: Hold stone with right hand about six inches in front of your solar plexus chakra. You should adjust the distance between the stone and your solar plexus chakra until you feel a tagging sensation there. Visualise a white flame burning and cleaning the stones. Hold it for around a minute.
Refrigerator Method: Put stones, especially jade, in the freezer compartment in your refrigerator. Just make sure they are separated from those frozen meat which often gives off denser and unclean energy. I know of a person who bought a small refrigerator for the purpose of cleaning stones.