December through March is the dry season — sunny, breezy, and busy with Colombian holidaymakers in late December and Easter week. April and November are good shoulder-season months: less crowded, mostly dry. The wet season (June to October) brings short afternoon downpours and rougher seas; boat trips to the San Bernardo islands may be cancelled.
The bioluminescent plankton is best seen on a dark, moonless night — schedule a visit around the new moon if it matters to you. Mosquito repellent is essential year-round; sand flies are worst in late afternoon.