The trail has been through-paddled by a four-pound Yorkshire terrier named Moxie. When I met Moxie on the Nulhegan she was having as much fun as my LabX was having. In the Allagash the rules are: “PETS must be under the owner’s control at all times and must not be left unattended. Pet owners are required to immediately clean up any fecal deposits left by their pets on campsites, trails, and in parking lots, and other developed areas, within the Restricted Zone.” You could look for the Adirondack Park’s dog rules. I think they are similar – those are the two most restrictive sections of the NFCT.
I have had happy paddling day trips with a dog in Vermont. I dislike sleeping with a wet dog and don’t usually camp with ours. I’ve met paddlers and dogs who have good manners and sense around traffic, bugs, other paddlers, and moose and other wildlife, and a few who do not.
The NFCT has some long carries, some rough ones, and some carries through towns and large campsites. I don’t how i would control a leashed dog while carrying a canoe, or even while wheeling a canoe along narrow roads with traffic such as you will encounter in places. With a new dog, kid, or other paddling partner I like to try things out with a few shorter trips before we dive into a longer one. Maybe you and your dog are old hands at this!
Also, I bet you need at least proof of rabies vaccination for a dog to cross the US-Canadian border in either direction.