Well, that depends on what New England should be. Considering the canon Federal seaboard supremacy and the portrayal in the East Map, I don't think New England in the "present" should be more than an ad-hoc grouping, that is only starting to develop a sense of traditional unity. Its current purpose is probably limited to common interests like collective trade terms/defense against the Canadians/Feds (which would actually require it to meet fairly often, handling war and peace on two fronts) but with the potential to evolve into more.
But then, what kind of iconography should this grouping aspire to?
The first option sounds more like the New England we know, but since New England is more economically marginal and more militarized the second option may predominate. But it's possible the New England grouping has aspects of both, maybe even a bicameral structure of military and trade interests.
- Should it be a congress of urban oligarchs, like the Low Countries States-General? Then maybe we go for a variation on Stadtholder, or some similar title that implies important duty without total supremacy/sovereignty. Maybe some old bureaucratic term like "Comptroller".
- Should it be a confederation of military orders, like the Teutonic and Livonian Orders? Then the top dog could be Grandmaster, or an Americanized version of that.
- Should it be a federal initiative to make governing New England easier, by granting one state de jure privileges over the others? Then Governor-General should be the most Baltimore is willing to grant.
- Should it be an extremely loose grouping like the old Swiss confederacy? If so... there may be no leader at all. Areas like Vermont probably already practice this.
I do like the idea of the bicameral focus on both military and trade, though with military slightly prioritized due to how marginal New England's position is when it comes to trade.
I just want to discuss how the transition from the states/counties only paying lip service to the "Comptroller-General" to the leader wielding actual power would go.
Where would the capital be? One of the major cities under New England control or a new city that arose in the new order?