Where does Lincoln say that the dredging of Charleston harbor is panicking the New York shipping and commercial interests? Saying that he's going to try to ignore secession and keep the federal government functioning in the south by collecting tariffs and delivering mail is far from the same thing.
Without comparative data from other ports, the 2k figure tells me little.
Fair enough. How about this, then? According to the 1878 edition of the US statistical abstract, in the table "Tonnage of American and Foreign Vessels entered at the principal and other seaports of the United States from Foreign Countries, from 1853 to 1878, inclusive", in 1859, 1.8 million tons of shipping entered New York harbor. In third place, (just behind Boston) with 659,000 tons, was New Orleans. Charleston had 129K tons, Savannah 86K, Mobile 131K, and Galveston 24K.Baltimore, whose status as northern or southern port is debatable, I suppose, had 189K.
It's interesting to note that the list of "principal seaports" includes five from the south and four from the north (not counting Baltimore in either).
http://www2.census.gov/prod2/statcomp/documents/
page 140
Good data, totalling the 8 mentioned ports, NYC accounted for almost exactly half! Amazing by any standard, the Southerners would have done well to use it as a model in developing their own shipping (were it not for the whole blockade thing).