I really like using LED's for this sort of thing. You can typically buy battery powered LED video light arrays for relatively cheap (< $50) that you can mount on a tripod and then adjust to give just the right lighting. That way, you can also blast your corals with lights from another angle, avoid reflections and really show off the shadows, you can also do fine adjustments to the lighting angle and intensity that, imo, make using a flash unit unwieldy. I have found that I can get much better results if I can tweak a constant light source instead of taking lot's of test shots with a flash unit or taking pictures with my halides which flicker constantly.
-Tre