Phonetic name given by the Spanish settlers to the god of chaos and disorder that the Taino indians in Puerto Rico (and also the Carib indians elsewhere in the Caribbean) believed controlled the weather, particularly hurricanes. From this we derive the Spanish name huracán and eventually the English word. As the pronunciation varied across various indigenous groups, there were many alternative names along the way. The OED mentions furacan, furican, haurachan, herycano, hurachano, hurricano, and so on.
The term makes an early appearance in Shakespeare's King Lear
(Act 3, Scene 2
Being the easternmost of the Greater Antilles, Puerto Rico is often in the path of many of the North Atlantic tropical storms and hurricanes which tend to come ashore on the east coast of the island. The taino believed that Juracan lived at the top of a rainforest peak called El Yunque (literally, the anvil but truly derived from the name of the taino god of order and creation, Yuquiyu) from where he stirred the winds and caused the waves to bristle.
On a side note, hurricanes in Puerto Rico were traditionally named after the saint whose feast it was when the storm made landfall. Notable ones include:
San Ciprian was one of the deadliest modern hurricanes, 247 dead, almost 5,000 wounded in Puerto Rico. It was also the last hurricane to hit the island that was named after a saint.