The Pilgrims, fielding a young side, were undone by a strong Magpies outfit.
To compound their woes, United had captain Owen Sheriff sent off for two yellow cards.
Boston (4-3-3): Jake Lovelace; Kelton Robinson (Flynn Slater 70), Owen Sheriff, Taylor Jaine, Lucas Stubbs (Josh Doran 81); Rueben Fogg, Han Stevens, Jake Henderson; JJ Ward, Jake Higginbottom, Patrik Bad (Jack Waddington 70). Sub (not used): Taylor Redman.
Referee: Simon Reast.