I'll wager the New England problem could be resolved by reordering the input data. GraphViz outputs are not independent of the ordering of inputs.
> New England is where it should be, but Vermont should be switched with Connecticut and Rhode Island.
NY -- PA, RI, VT
New York borders Connecticut, but not Rhode Island.Google maps shows a border.
https://www.google.com/maps/place/Long+Island+Sound/@41.3418...