Well energy (and kinetic) is mitigated by armor. The elemental (and internal) are not, and will hit harder even with full armor debuffing. Afaik,the elemental (or internal) are always better with the exception of merc's/troopers who use the armor penetration stance.
But since I have no sent/mara to test with and neither understand your class mechanics nor have I bothered reading about classes i dont currently play, you should really test for yourself or consult your own forums on the issue.
The fact that you do energy damage is irrelevant. I do internal and kinetic damage on my sage yet the elemental one is better. On my slinger, who does mostly energy (and internal for dirty fighting) damage the internal is better.
Focus guard/rage jugg also get armor pen in spec, and can use the energy proc. Carnage/combat gets 100% arm pen for a few seconds every 15 secs. Haven't done the math to see which relic is best for those specs tho.