I'll link you to PeaRidge's excellent synopsis of what the government did which impacted Southern shipbuilding.
https://freerepublic.com/focus/news/3443027/posts?page=929#929
Missing is the fact that smaller New England ports -- Salem, Newburyport, etc. -- also went into decline in the early 19th century.
The advantage at the time was to larger ports with extensive rail connections and large economic hinterlands: New York, Baltimore, Boston, Philadelphia.
Charleston and Savannah didn't develop their rail connections. The free population was smaller and more sparsely settled.
Still, there was regular shipping between Charleston and foreign ports. James Adger, a Charleston shipper, was at one point the fourth-richest man in America. George Trenholm, another Charleston shipper, was also one of the richest men in the country.
nice recap except the premise of the 1817 navigation act being passed to boost Northern shipping is wrong. The act was passed in retaliation for the British barring American shipping from trading between with their Caribbean islands.