The interior area of the ship used to detain prisoners & stowaways, and to punish delinquent crew members is known as the brig. The brig usually resembles a prison-cell with bars and a locked, hinged door.
On the other hand, a ship dedicated to containing prisoners may be called a prison hulk.
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Note that the term "brig" is carried over to all Naval prisons - even those ashore.
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Because they were ships? Do you mean longships? They were long and thin.
The ships were called privateers. The authorisations were called letters of marque.
On the River Thames between Blckfriers Bridge and Greenwich