There are currently two good ways to obtain Energy Crystals, and we'll look at both of these below.
Get Energy Crystals from eventsThe only way to reliably get Energy Crystals at low levels is to do events that randomly appear in your world. These are available for a limited time, and many of these either has enemies that has a decent chance to drop Energy Crystals (look mainly for the Araktula Invasion Event if you want to farm mobs. These have a 5 % drop chance each), or they reward you with Energy Crystals for completing them.
Event Chests also seem to have a good drop rate for Energy Crystals, so make sure to always loot these!
All the Storm Events (such as Sand Storm or Electro Thunder Storm) requires you to destroy three Crystals, and each of these crystals will drop one Energy Crystal each. So these are also good to look out for, since you get a guaranteed 3 Energy Crystals for doing a 5 minute event.
You can of course also do this method at higher levels or even at max level, but the option below will give you a better return on Energy Crystals per hour if you are able to do it.
Get Energy Crystals from Tomb of C’ThirisThe Tomb of C’Thiris is an end-game area with level 35 monsters, so this is not somewhere you want to go before you have reached level cap, and got yourself some decent gear. You can get to this area by crafting a C’Thiris Tesseract at Altar IV. This item costs 10 x Stone and 1x Energy Crystal to craft, so it's not a good option for getting Energy Crystals if you don't already have a single one.
Look for sarcophagi in Tomb of C’Thiris, and open these with your pickaxe to get some loot. While most of these won't give you Energy Crystals, some of them will, so keep looking for these and open them to get a lot of Energy Crystals.
All monsters in this area has a chance to drop Energy Crystals as well, but far less frequently compared to opening sarcophagi. I would not advise anyone to farm enemies to get Energy Crystals, but instead look at it as a bonus if you get one from randomly killing an enemy.