Yes, Elnoyles are the best source for Energy Crystals.

In Esthar City, there's a man dressed in black sitting on the railing of the walkway in an area on the city's right side between the middle and the shopping mall, during and after the Lunatic Pandora going over Esthar. Talk to him, and it'll result in an Elnoyle fight, and it'll always drop an energy crystal or two. Leave the the screen, and he'll be there again, so you can keep fighting him as much as you want.