At the end of our cruise we flew from San Juan to Vieques and did a tour of their Biolumenescent Bay. This bay (and a few others within the tropics) has an incredibly high concentration of dynoflagelites that glow when disturbed. It was so worth the trip. To do this during a cruise would require an overnight in San Juan and quite a bit of distance to cover.
And maybe it is a good thing. There is a bio bay on the main island but it is being affected by development. Adding big trips of cruise passengers might add more stress on the bay than Mother Nature can survive.