It’s a good idea to cleanse all the energy that the stone may have picked up on its journey to You. In cleansing its energy, you prepare it for a new life and purpose.

To cleanse a stone is to remove the energy that a stone has absorbed and return it to a clean, pure energy. To charge a stone is to replenish its energy after it has been depleted. Though some use these words interchangeably, a stone must often be cleansed before it can be charged.  Here are the methods you can use.
MOONLIGHT - Full Moon: I have not yet met a crystal that does not enjoy the moonlight. The best time is during a Full Moon. The strong full moon energy lasts for 3 days, so it's OK if you miss the actual day of a full moon. You can catch those moonlight rays on the day before. This will not only cleanse but recharges your stones.

Full Moon Calendar here
SOUND: Everything has a vibration, especially sound. Since we are helping to set a crystal's vibrations back to its original state, it makes sense that sound can help us with that. Crystal or Tibetan singing bowls work perfectly. Have your crystals near the bowl as you play it. You can run a tuning fork over your crystals, use a bell, tingshas (Tibetan cymbals), or drums. Any loud music will work as well. Put your crystals in front of the speakers and turn up your favorite music. The important thing with sound cleansing is to have the crystals within the sound's vibrations.
REIKI: You can cleanse and give your crystals an extra little energy boost with Reiki energy. Simply hold the crystals in between your hands as you and infusing them with the energy.
SAGE AND INCENSE: Sage is another wonderful energy cleanser. You simply run your crystals through the smoke or waft the smoke over your crystals. This method also cleanses any of the areas around your house. If you do not have a stick of sage available incense work also.
OTHER CRYSTALS: Your crystals can be placed on top of an Amethyst Druze or cluster, put in a bag with a tumbled Carnelian, or surrounded by Clear Quartz Points. Keep in mind these crystals mentioned above will need to be cleansed themselves. But it is so nice that they can help out the other crystals we work with.
SUNLIGHT: Many crystals love to sunbathe, especially ones that are red, orange or yellow (like Carnelian and Sunstone ). You can put them out in the sun for a few hours for a cleansing and recharge. However, be careful of which ones you place out in the sun. There are some crystals that will fade in sunlight or change color. Typically, these are the pigmented crystals, see-through crystals that have color, like Amethyst or Fluorite. If you are not sure if a crystal will fade or not, then be safe and keep them out of the sun.
***Avoid Sunlight: These crystals should avoid being placed in sunlight for prolonged periods of time. This list will include many of the most common crystals. This list is not exhaustive, but it will give you a good start.
Amegreen, Amethyst, Ametrine, Apophyllite Green, Aquamarine, Auralite23, Celestite, Citrine, Fluorite, Hiddenite, Kunzite, Opal (will dry out), Prasiolite, Rose Quartz, Smoky Quartz, Spirit Quartz, Super Seven, Topaz, Turquoise.
WATER: A nice cool water bath works very nicely on most crystals, or place them under running water. It is quick, easy and you can do it anytime. When I run my crystals under running tap water in the sink I visualize the water cleaning out any negative energy. This will get them clean physically as well as cleanse their energies. Keep in mind that there are some crystals that you need to avoid putting in water. A good general rule of thumb is to not submerge crystals with a MOH hardness level of 5 or less. Also if you are going to keep the crystal in the water for a long period of time, make sure it does not contain iron -- like Hematite, Magnetite, and Lodestone -- because it can cause them to oxidize.

***Avoid Water: The following is a list of some of the more common crystals that should completely avoid water. Water can either damage the crystal or cause the crystal to disintegrate and dissolve. This list is not exhaustive, but it will give you a good start. Also, avoid water if you have charms or other metals attached to it.
Desert Rose, Halite, Himalayan Salt (Salt Lamps), Malachite, Selenite

 source: Various online research