Two goals from Leon Squire and one apiece from Jacob Pease and Corey Newman saw the Pilgrims overturn a 1-0 half-time deficit to record only their second win of the league season.
There was also a debut for 16-year-old goalkeeper Will Bromfield.
Boston (4-3-3): Will Bromfield; Daniel Worthington, Billy Hodgkiss, Joe Cain, Corey Newman; Miles Lynch (Harry Bunce 61), Jacob Pease, Aaron Eyett; Leon Squire, Liam Moran (Steven Dovey 55), Bradley Easey (Karolis Andriulionis 25).