ACA's Atlantic Coast route has a Boston Spur that you could take to the main part of the route and then follow that north to hook up with the Nothern Tier in Brunskwick, Maine. That would add some time, though.
One option is Amtrak's Downeaster train service. You can roll your bike on (i.e., you don't have to box it) and go from to Brunswick. This subject came up on antoher forum recently. According to Amtrakm you cannot detrain at the Freeport, Maine station but you can at Portland and Brunswick.
Here is the link to the train information:http://www.amtrak.com/downeaster-train
It's only a 3.5 hr. ride to Brunskwick, and there is a convenient 9 a.m. departure. There are internal links on the page for the schedule and bike information.
Starting from somewhere like Brunskwick would allow you to ride through New Hampshire, Vermont and the Adirondaks in New York. Very pretty part of the route. Vermont especially so.