What is the black ship?

The term "black ship" in this story is used to refer to
any of the ships that was used (usually only once a year) to ferry money and some goods
from Asia back to Europe.

During the time in which this
story is set, Spain was the only European country with a real presence in East Asia. 
Therefore it had a monopoly on trade there.  Each year, a ship would go from Asia back
to Spain carrying the money that had been made in that year's trading.  The ship
belonged to the Spanish government/crown.

Because the ship
had such huge amounts of money, it made a very tempting target for people like
Blackthorne and losing it would be a giant blow to Spain.