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One thing to consider about those defenses - ITTL, the Formerly United States just lost Norfolk (and what, 75% or so of their Atlantic coast, if you count the Gulf?), and they need to replace it. New York City is reasonably centralized along what is left of the Union's Atlantic holdings, and seems to be a strong choice for the primary naval base - so most of those fortifications could be needed, anyway, just to protect the Navy while it's in port.
I really don't think the naval vulnerability would be a major consideration. "Too isolated" is enough on its own.