The league was superseded by the Canadian American Association of Professional Baseball, which its members joined for the 2005 season.
Albany (Albany Diamond Dogs), Glens Falls (Adirondack Lumberjacks), Yonkers (Yonkers Hoot Owls), Newburgh (Newburgh Night Hawks), Little Falls (Mohawk Valley Landsharks) and Mountaindale (Sullivan Mountain Lions) were all given teams and Adirondack won the first league championship in a 68-game season.
The Mountain Lions were sold to a new ownership group who renamed them the Catskill Cougars and moved them to the North Atlantic League while the Landsharks moved to West Warwick, Rhode Island, expanding the league into New England as the team became the Rhode Island Tiger Sharks.
After the four-year merger, the Northeast League returned to its status as a separate entity following the 2002 season.
The Adirondack Lumberjacks relocated to Bangor, returning a team to Maine for the first time since the Blue Ox folded.
The Mad Dogs were bought by Jonathan Fleisig, who moved the team to Pittsfield, Massachusetts, where they played in Wahconah Park as the Berkshire Black Bears.
New Jersey, Brockton, North Shore, New Haven, Quebec, and Elmira became part of the Canadian American Association of Professional Baseball (or Can-Am League) along with an expansion franchise in Worcester, Massachusetts, and a traveling team formed when Bangor's charter for the new league was rescinded.