I believe any time is good. If you decide to go in the fall months (at least september) there’s a particularly high a chance of a hurricane so I suggest coming in spring or early summer.

Also I’m not sure if I remember this correctly but I’ve heard that it’s better to visit the bioluminescent bay during the new moon phase. It allows you to see the organisms so much better.

Anytime there is a new moon is good. Also, it’s nice to time it to when the moon is rising later in the night. The trip I took was at 8ish but the moon didn’t “rise” until after 11:30 making the visit just as good as if it was a new moon.
As a heads up, the electric boat was struck by lightning recently and burnt so the only trips available as of Dec. 2006 are by kayak.