The honest comparison
There is no single winner because the three experiences solve different travel problems.
Puerto Rico has three major year-round Bio Bay destinations: Mosquito Bay on Vieques, Laguna Grande in Fajardo, and La Parguera in Lajas. They all rely on bioluminescent dinoflagellates, but the logistics and style of the visit are different.
If your only criterion is “brightest,” Vieques deserves serious consideration. If you are staying around San Juan and want the shortest mainland transfer, Fajardo is usually the logical choice. If you are staying in western or southern Puerto Rico and want a private boat-based evening, La Parguera is often the practical fit.
The best Bio Bay is the one that fits your location, preferred tour style, available time, and expectations.

