You mention that you have great flexibility with how much time you can spend. Do you have the same amount of flexibility with your budget? It's a pricey time to visit Boston, New England and also New York. Cape Cod and Martha's Vineyard will be more affordable (it's not high season).

If you have a particular budget in mind, that would affect recommendations for where to go and how much time to spend. You could easily spend 3 weeks in the region.

For booking hotels, it will be too early for most places (including NYC and Boston), but not too early for especially desirable inns and resorts in the popular fall foliage areas.

Accommodations can be made thru airbnb, as much as a year ahead. We have used airbnb this past summer and had wonderful accommodations.

Airbnb is a good option for all areas except New York City. NYC has laws that make most short term vacation apartment rentals illegal.