A ship is any large watercraft. Ships are generally distinguished from boats by their capacity (passengers or goods). They are (normally) swimming unlike floating submarines and hovercrafts. Ships have an organized crew with different functions and command levels, while boats have a maximum of a leader (coxswain, steering man).
Another approach is that if one watercraft can carry another one, the bigger one is called a ship.
There are some exceptions for historical reasons.Watercrafts operating normally on lakes, rivers or other protected water areas are called boats even if they are nowadays big enough to carry themself.
It is a traditional (british) practice to call a ship a "she" or as "her", even if she is named after a man.
List of books: Ship