I'm a Canadian and I've owned boats on both sides of the border. You can't continue US Documentation, but no issues with state registration that I'm aware of. You can't bring a boat you own into Canada without declaring it and paying HST (or applicable GST and PST) on entry, regardless of where it is registered/licensed.
I bought a trawler in the US last fall and immediately registered it in Canada. When I entered Canada in the spring I paid the HST. No issues. It's easier than bring a car or trailer in. If the boat was built in North America there are no duties.