In 1789, how did the economy of the Mid-Atlantic states differ from the other regions?

The economies of New England, the deep South and the Mid-Atlantic states all involved small farms and towns with small manufactories and merchants, but there were differences.  In New England the economy centered on small farming communities, with the larger towns having merchants and manufactories, and some mining operations in the hills.  The deep South, of course, was economically tied to small family farms and the large plantations with their cash crops, which before the invention of the cotton gin were largely hemp and tobacco.  Cotton became "King" after Eli Whitney's invention made the mass processing of cotton financially feasible.

The Mid-Atlantic states' primary agricultural products were grains (except Virginia, which was the premier Southern plantation state and so grew much hemp and tobacco), and this was much of the basis of the shipping businesses in large towns and cities on the coast.    The grain economy of these states had been severely disrupted by the French and Indian War and worse by the Revolution.  There were boom prices early in the Revolution, but after the British seized Philadelphia in 1777 Washington's confiscation of millstones (to prevent the British gaining supplies) and later British depredations (and blockade) caused great disruption.  The lower Delaware Valley came out of the war a little better than other areas, but the economy was in tatters at the end of the Revolution.

In the 1780s the war between France and Britain caused great opportunities for the grain trade of the Mid-Atlantic states, but risks also.  Seizures at sea of grain by the French navy led to a brief and undeclared naval war between the United States and France in the next decade, problems with Britain contributed to the war of 1812 later.  In 1789 the grain trade in the Mid-Atlantic states had recovered from the Revolution and was not yet too damaged by the troubles in Europe.  Things were relatively smooth for the large farmers in the Mid-Atlantic, and the shipping business was doing well in consequence.  The large shipping businesses in New York and down the coast from there were prosperous at this time.  Smuggling had been brought largely under control by the local governments and the US, something the British had never been able to accomplish in their colonies.

The first link below is to the National Archives and Records Administration, which has a great many records on this subject and much more.