'Safe Harbor' is the district with docks that is considered "international waters", where any ship can find harbor and buy help/repairs, crew can get medical assistance.
'Safe Harbor' was meant to be a safe place for political meetings, but ended up being something like pirate-owned part of the city, somewhat outside the law, because Unity themselves would host any political meetings between other countries and take bounty/praise for this. 'Safe Harbor' is separated from the city proper, and to enter the city a ship and crew must pass the inspection that is conducted by the Blue Jackets. Any regular and expected ships would go straight to the Pearl docks, bypassing the 'Safe Harbor'.
'Safe Harbor' is a part of the city Unity still likes to keep and benefit from.