America's first permanent establishment

I don't know the answer to the question at large, but this statement is incorrect. Saint Augustine, Florida is the oldest permanent European settlement in North America.

Some of it comes down to issues with the location. It is literally in a swamp to begin with, so the general area is less than pleasant in addition to problems with construction or expansion. The peninsula it's on makes traveling to it more difficult than a centrally located capital, as many are (part of the reason the capital moved to Richmond in 1780). Looking at most large cities of the 17th and 18th centuries, they're large port cities. Norfolk port develops at the mouth of the James River, but on the other side. There is also a port just a little South of Jamestown which is still used as a dockyard today, but Jamestown itself never developed the necessary port. New York (originally New Amsterdam) grew so large because, in the start, it was a large Dutch port. Both Boston and Philadelphia were port cities as well. Once the capital moves to Williamsburg, and then Richmond, there's not much reason to develop the area during the big industrial booms of the 19th and 20th centuries.

I have no idea what you mean 'as far as NYC, I know at that point things were kind of more planned out for "America." NYC was settled like 11 years after Jamestown and it was pretty small and feeble for the first 60 or so years of settlement, especially when it was ruled by the Dutch