Yeah, I figured it was some type of plankton, because I wasn't able to see anything where the flashes were coming from. I did look up pistol shrimp at first, but saw that humans couldn't see the light formed from their bubble popping.
StirCrayzy, I did manage to catch one pistol shrimp by putting the rock in question in a high salinity dip for 20-30 seconds. I know there was more than one in that rock, so it wasn't terribly effective for me (only one came out). I've been trying to find a way to lure them out without removing the rock from the aquarium, so far no luck, though.
I tried and tried to catch pictures of the bioluminescence, but I wasn't able to. Tried with my camera at first, then somehow got my father-in-law to loan me his SLR camera with a really fast lens (he's a professional photographer). That still wasn't enough. The light isn't very bright, visible to me when my eyes are adjusted to the dark, but not bright enough to register on a camera, unfortunately.