Holbox has no cars and no reef. What it has is the point where the Caribbean meets the Gulf of Mexico, and the plankton bloom that comes with it.
Whale sharks are the season, roughly mid-May to mid-September. Boats run an hour or more offshore to where the sharks feed at the surface; you snorkel in pairs with a guide, you do not dive, and you do not touch. The permit window is fixed by the regulator and operators outside it are selling something else.
The three-stop lagoon tour runs year-round: the Yalahau cenote, a freshwater spring the pirates are said to have used, Isla Pájaros for the frigatebirds and flamingos, and Isla de la Pasión. Flamingos are most reliable in summer.
After dark between roughly July and January, the bioluminescent plankton in the shallows off Punta Cocos light up when you move through them — a walk, not a boat trip, and best on a moonless night.
The island is also a serious kitesurfing spot in the winter wind, and the shallow lagoon side is about the most forgiving water a beginner could ask for.