Goals from Finley McDaid and Sam Finch overturned a half-time deficit and secure all three points for the Pilgrims.
The result completed a league double for United, who were 2-0 victors in the northeast in November.
Boston: Sam Buckland (Alfie Harney 50), Daniel Fisk, Tyreece Keating, Harrison Guest, Finley McDaid (Lake Taylor-Peak 80), Elod Nadasdi, Aron Ealham, Toby Foreman, Sam Finch, Josh Panton, Denis Matei (Jack Dixon 70).
Referee: Peter Brothwell.