I think you have several options for getting from the Northern Tier to Boston.
Probably the most direct route is New York bike route #5 to US route 20 to MA state route 9. Once east of Quabin check out Rubel's bike maps to get you off the busy roads and onto better local roads for biking.
Got a little more time, then continue the Northern Tier to Ticonderoga, then go through Rutland Vermont and follow state route 103 across the green mountains. Then Bellows Falls to Keene NH, and into Boston basically on Route 119.
Got a little more time, then continue on the Northern Tier to Sharon Vermont, and then follow US Route 5 to Bellows Falls, and then onto Boston as above.
Got more time, then follow the Northern Tier over the Kanc to Conway NH, and go to Portland ME before picking up the Atlantic Coast Route towards Boston.
Or, go all the way to Damarascota ME and pick up the Atlantic coast Route directly.