First half goals from Dave Iwediuno and George Smith plus a second half bullet free-kick from Lee Allinson handed the Waders a notable victory.
Spencer Weir-Daley replied on 40 minutes for Boston, who also lost the services of midfielder Ben Milnes to a head injury during the first half.
Boston (4-4-2): Ashley Timms; Conor Marshall (Peter Bore 65), Scott Garner, Carl Piergianni, Netan Sansara; Ben Fairclough (Charley Sanders 65), Ben Milnes (James Reed 30), Ian Ross (Jordan Nuttell 74), Ricky Miller; Marc Newsham, Spencer Weir-Daley. Subs (not used): Elliott Green, Sam Vince (gk).
Referee: Shaun Barry