Which of the bioluminescence bays are the best to see and negotiate in Puerto Rico?
According to this website (http://biobaypuertorico.com/), the one off the island of Vieques is the most active one, followed by Fajardo and La Parguera. I can't compare because we only went to La Parguera but I can say it is a fascinating experience that I won't forget. Not sure if you're planning to kayak or swim but we were on a tour boat so just got to watch pros dive and swim to see the bioluminescence from their actions.
I have been to PR often, as my wife's family is from there and I visited nearly every corner of it. I like Vieques' bay the best. Actually I find Vieques (especially the village of Esperanza) the best place to spend a holiday in PR. Next time we go, after visiting family, Esperanza is where I want to go (been 3 or 4 times already, but not tired of it). There are no fancy hotels on that side of Vieques, but several B&B have opened up. It's a rural, undeveloped and peaceful little village. Perfect for a 3 day getaway. I find much of the big island of PR too crowded and many beaches not too clean. You can fly to Vieques or take a ferry from Fajardo. Done both but I'd rather fly, way faster. There are taxis in the island, so you don't really need a car. The bioluminescent bay is near Esperanza on the south shore of Vieques, through a dirt road east of the beautiful Sun Bay (aka Sonbe') beach park. When I went there was a local guy organizing the tour with a very very old mini bus. It was fun, but the mosquitoes will eat you alive. Bring plenty of repellant.
We went to Vieques to see the bay. We took a day trip from San Juan (we had a car) and then got an organized trip which included return transport to the island, dinner, transport to the bay and on the bay.
The only thing is that you have to hope for a good clear night and a fairly full moon to get the full effect. We didn't have the best conditions, but it was memorable.