At the risk of oversimplifying a lot of history and early consolidations and corporate name changes, the Air Line name was historically applied to the trackage between New Haven and Willimantic via Middletown, which was part of a through route between Boston and New York that also involved what became the New York & New England RR east of Willimantic and the New York, New Haven & Hartford west of New Haven. The heyday of Boston-New York passenger service over the Air Line was the 1880s-1890s and through service ended in 1924. Passenger service via the New Haven RR's Midland route (Boston-Franklin-Putnam-Willimantic-Hartford) lasted until the big flood of August 19, 1955 took out a bridge just west of Putnam that was never replaced, although by then it was down to a single daily round trip by a solo RDC. Both of these "inland" routes between Boston and New Haven became secondary once the Shore Line was completed as an all-rail route with the bridging of the Thames River at New London, replacing ferries.
The New York & New England's primary entry to Boston in the late 19th century was the current MBTA Franklin line and Dorchester branch (Fairmount line), and that was the route of the Boston-New York New England Limited (the "White Train"). The Charles River RR was a secondary line for the NY&NE and I don't believe it ever carried any long distance trains.
