In-form Zac Hardy, fresh from his FA Youth Cup hat-trick, was on target twice for the Pilgrims, with all four goals in the match scored in the first half at Wigginton Road.
The result extended United's unbeaten start to the league campaign.
Boston: Austin Barker, Finley Hipkin (Daniel Bridges 85), Oliver Houlston, Dexter Tomlinson, Charlie Brooks, Kirils Snikeris, Rueben Fogg (Sean Bray-Smith 60), Jake Thompson, Will Pettitt, Zac Hardy (Ryan Makings 70), Rhys Smaller (Lewis Greenfield 46). Sub (not used): Zach Marsh (gk).
Referee: Craig Atkin.