The cleansing method which you use is always a matter of personal choice, sometimes dependent upon the amount of time which you have readily available, but I strongly recommend that you use one of the following cleansing methods which I myself have found to be very successful.
Sea Salt Dry- Use with caution. This is probably the best all around method to use. Sea salt may be caustic to some softer Stones, damage finishes on Stones, or effect the encasing of jewelry Stones. If you live near an ocean you can use the ocean itself to clean your Stone but as many of us do not we must settle for purchasing sea salt. Do not use table salt since it contains additions that are not in the best interest of cleaning your Stone. Place the Stone with the point downward in the sea salt and leave 24 hours.
Sea Salt Wet - Use with caution. Sea salt may be caustic to some softer Stones, damage finishes on Stones, or effect the encasing of jewelry Stones. Most importantly is to use running water. Do not use tap water. Use 1/2 cup of sea salt to 1 cup natural running water. Allow to soak 8-24 hours depending on the Stone and the need. Allow to dry natural either in the sun or moonlight depending on the Stone.
Sea / Spring / Lake / Rivers - If you leave near the sea, you can soak the Crystals in the sea water for 3 to 4 hours. After that, energize them under the sun. The Crystals can resume their vibrant rather quickly using this method. Crystals love to interact with the nature. Likewise, if you live near the flowing rivers, lakes or springs, you can also do the same thing. Make sure that the sea/lake/streams/rivers are not polluted or else you will be contaminating the Crystals instead.
Sunlight - The Sun can be a very strong energetic way to cleanse your Stones. Sunlight is terrific for clear Quartz. After a sunbath on your windowsill, your clear Quartz Crystals will be noticeably brighter. Dark, opaque Stones like black tourmaline and obsidian can also be recharged by this method. This is an excellent technique for quickly energizing personal Stones. I suggest not leaving the Stones out in the sunlight for more than 8 hours at a time as well.
Moonlight - I almost always use this method to clear and charge my Crystals. The moon light from a full moon is especially powerful at cleansing your Crystals and recharging them. I suggest putting them outside on the night of the full moon and taking them back into the house before noon at least because after the noon day sun it becomes draining to the Crystals energies. You can also place them outside during a new moon and cleanse them that way. I like this method of cleansing my Stones because every two weeks there is a full or new moon and I am always reminded at that time to cleanse and recharge my Crystals.
Smudging - You can use sweet grass, sage, or even incense to smudge your Crystals. Now begin to burn it until a good strong smoke is coming from your sage. Hold the Crystal, gem or pendulum in this smoke for at least one minute and preferably three or four minutes. This clears all negative energies that have become attached to this Stone but does not energize the gem or Crystal. To re-energize the Stone, place it in a window so it can be exposed to the rays of the sun and moon. Remember, they re-energize even when it’s cloudy.
White Sage is the only herb that I use to cleanse. Others may recommend other herbs but I find that White Sage guarantees that the cleansing will be deep and complete.
Mother Earth - You can bury your Crystals in the Earth and leave them there for 24 hours. Crystals and Gemstones come from the Earth so when you use this method it is as if you are giving them a little vacation from home and they are rejuvenating and reviving themselves as they spend time back in the Earth. Be sure to mark your Crystals where you bury them as to not lose them and also remember that the Earth contains moisture so for those Stones that should not be put into water it could affect or scratch them. You can also get a container of Earth and place that container of Earth in your home while you bury your Crystals and allow them to recharge, this method is good for those living in an apartment or somewhere they do not have a yard of their own.
Flowers - You can also soak Crystals in flowers such as rose petals, carnations etc for 24 hours. The flower essence removes the negativity and cleanses the Crystals. And of course, the purity and energy of the flowers will be transmitted to the Crystals.
Cleansing By Using Your Intention - For those who are practiced in using intent to make energetic changes, place the Crystals or gems in front of you, focus your mental energies upon these Stones, and ask the powers of the Universe to cleanse them of all negative energies and to re-energize your Stones for their maximum potential. This method however requires much concentration and focus and you need to practice for some time to ensure whatever you are trying to clear is actually cleared. And please remember to thank the Universe for doing this beautiful work for you.