Boss Ships are vessels that carry much more firepower and heavier armor than standard ships in the Caribbean. There are a few Boss Ships a pirate may encounter, including the Ships of the Line that appear in the Treasure Fleets. These Royal Navy and East India Trading Company vessels are not encountered without a group of heavily armed escorts, making them a very difficult target to destroy.
Further there is The Queen Anne's Revenge that appears in the Caribbean from time to time.
Currently, no boss ships exist in the service of Jolly Roger.