The reason that many of these cities are where they are isnt because of sea lanes, its because of either a needed resource or else 'power". There are natural features on the US East Coast called the "Fall zones", Heres where the rocks and higher topography of the outer Piedmont terrains, give way to the Coastal Plain.
That abrupt change in elevation cause natural water falls to exist in the drainage patterns of streams and rivers. The Fall Zones are where the colonials would locate their grain , textile, and lumber mills because they harnessed water power and here was where they got the most bang for their buck in power .
If you look at maps of all the coastal plain states, youll see that in each state, at their areas of the FAll Zones, there were hundreds, nay , thousands of old water power dams.
Skidding raw materials to mills was as important as shipping in raw materials from abroad . So, like today, transporting goods to ships was more easily accomplished by wagon over short distances between the mills and the docks than it was to create shallow draft hydraulic dams near the coasts.
Thats just a guess why the cities are where they are. The fact that, as previously stated, the Diamond Shoals and the Columbia Bar Shoals are the two deadliest stretches of water in the US make them less attractive as big seaport areas. (The whole ALbermarle and Pamlico sounds are just big swamp lined embayments like the Tidewater and Jersey SHore). Dredging is always a PITA for shallow embayments.