It appears that Boston Harbor will become the connection between North Station and the Seaport via new ferry service.
According to Curbed Boston, “The Massachusetts Convention Center Authority and a handful of private companies, including Vertex, are working toward launching weekday ferry service from Lovejoy Wharf near North Station to the Seaport District-slash-South Boston waterfront…The authority has issued a request for proposals to underwrite the service for a year, with an eye toward extending it for three additional years. If the authority can line up the private funding—and it looks like it can—then service could start in late August or September.”
You can read more on Curbed, here.