There aren't very many traditional boss battles in Assassin's Creed 4: Black Flag. However, the few that you'll find can be difficult if you don't know how to properly approach the battle. The El Tiburon boss battle at the end of Sequence 12, Memory 3 is one such battle.
Once you tail El Tiburón and Torres to the fortress, head to the rooftop and take out any guards in your immediate way. You can take out all of the guards on the roof, but it's not necessary. Move over to the rope running above Torres and assassinate him from above. Unfortunately, it was a fake and you now have to deal with El Tiburón.