There are many ways to clear crystals of negative energy. Here are some suggestions:
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.
If small, can place on a Quartz or Amethyst cluster
(This is a great way to clean necklaces! Cluster should be dedicated to 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 too!
Sage Tea Method:
This can be very effective with less possibility of damaging them. Since there are many crows and other such birds who love bright shiny objects where she lives she found out the hard way that setting them outside to wash in the rain and bask in the sun (or under moonlight) was not going to work for her.
Take some 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 and pour the cooled tea over them. Leave overnight, then remove them and rinse with clean and pure water. Since there are chemicals in most water systems you may wish to buy a gallon of distilled water at the store for under $1.00.
If you can safely place them outside for nature to cleanse that is perfect, though you'll need to be able to distinguish which stones cleanse best by moonlight and which are more solar.
Pass stones through the smoke of a scented incense such as sweetgrass, frankincense, sage or Dragon's Blood or passing them through a candle flame.
Place stones under alternating hot & cold running water for 5 minutes (or in the rain for many hours). I place stones in a plastic strainer and then alternate the hot and cold running water from the sink. It is good to have a water filter on your tap to filter out some of the chemicals if possible.
This is quick and easy but there are drawbacks: some stones loose their coatings when they get wet such as Lapis, Malachite and Sodalite. They often are stronger after this is done -- but they may get damaged faster. Cleaning these stones in the sun or moonlight works fine. [Stones really really like the rain. It cleans them much better than the sink method if the weather is cooperating.]
Sea salt method:
Use about 1 cup of sea salt to 2 cups natural spring water. I place my stones in the salt, and let them soak for the better part of the day. If the day is sunny, I try to let them dry in the sunshine for a few hours, or if there are lunar stones, to lay in the moonlight on a windowsill through the night.
When all else fails... or you are having a hard time cleaning something, bury it in moist sand (or soil). No wrappings. Beware, polish is often removed doing this method. However, it will get something clean.
Stones Damaged in Sunlight (there may be more):
translucent types often lose color
pink variety fades
brown or orange types may change to pale pink
may change color
green and purple types change color
becomes pale or loses color
~From Maat's Book of Shadows