There are many ways to clean crystals of negative energy.
Here are some suggestions
Position in sunlight, moonlight or rain (see water method) for up to a day. Placing the stone on or near a plant often quickens the process.
If the stone is small, place it on a quartz or amethyst cluster. The bunch should be dedicated to this purpose with a clear intention. Clean your cluster every month or two in rain or sunlight if possible. Amethyst geodes work well too. This is a great way to clean necklaces!
Sage tea method:
This is very effectual with less possibility of damaging crystals. Take fresh sage if available and brew a pot of light tea; allow it to cool. Place your crystals in a bowl (use glass if possible) and pour the cooled tea over them. Leave them in the sage tea overnight. Then remove them and rinse with clean, pure water. As there are chemicals in most water systems you may prefer to use a gallon of distilled water.
If you can safely place crystals outside for nature to cleanse that is perfect, though youll need to be able to distinguish which stones cleanse best by moonlight and which stones cleanse best by solar.
Pass stones through the smoke of a scented incense such as sweetgrass, frankincense, sage or Dragons Blood. Passing them through a candle flame also works.
Place stones under alternating hot and cold running water for 5 minutes (or in the rain for many hours). 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 chemicals. This is quick and easy but has drawbacks: some stones loose their coatings when they get wet. Use vigilance with lapis, malachite and sodalight as they may get damaged faster. Cleaning these stones in the sun or moonlight works fine. [Note: Stones really like the rain. It cleans much better than the usual water method when the weather cooperates.]
Some homeopathic solutions clean gemstones as well. Use NET (alcohol-free) homeopathics to clean stones. Other alcohol-free brands may work as well.
Sea salt method:
Use 1 cup of sea salt to 2 cups natural spring water. Place stones in the salt, and let them soak for the better part of the day. If the day is sunny, let them dry in the sunshine for a few hours, or if you have lunar stones, lay in the moonlight on a windowsill through the night.
When all this fall short or you are having a hard time cleaning something, bury it in moist sand (or soil). No wrappings. It will get gems clean but be aware that the polish is often removed when this method is used.