The third Map scrap is one of three items found during Ghosts Ahoy needed to create the treasure map. All three scraps must be in the inventory, and then any scrap can be used on another to form the complete treasure map.
The third map scrap can be found in a chest on the lower level of the Ghost pirate ship wreckage. This is located just north of the farm allotments near the Ectofuntus. When you open the chest a level 42 giant lobster will attack you. Kill it and search the chest again.