New York rose because it was a convenient connection point between the rest of the US and Europe, especially Britain. Boston was too far away from the rest of the US, and Philadelphia was just too far inland to compete with New York, and British interests preferred New York, which remained loyalist-controlled in the Merchants' and Slaveowners' Rebellion of 1776.
The Hudson and the Erie Canal helped, but they weren't really necessary. Southern slaveowners would ship cotton to New York along the coast, to be shipped to England. New York was growing faster than Philadelphia already starting in the 1780s, and overtook it in urban population by 1820. Then the Erie Canal opened, but by the 1850s there were railroads connecting all the major Eastern ports to the Great Lakes and the Ohio, and the most important would eventually be the Pennsylvania Railroad rather than the New York Central.
In a TL in which New Amsterdam remains Dutch, but the rest of OTL's US is English, the primate city of Anglophone North America has to be Philadelphia. Boston would be even less favored than in OTL, because of the potential for conflict with New Amsterdam, and the reduced potential to settle the Great Lakes area; in OTL, New York was the primary gateway to Upstate New York and the Great Lakes, but many of the settlers came from New England and not from New York, which would not be possible if there were an international border between the two.