Margetts struck after nine and 12 minutes before sealing his hat-trick from the spot two minutes before the break.
United were much-improved after the interval but they did not come closer than rattling the crossbar in the first half through Cameron Johnson.
Boston (4-2-3-1): Michael Emery; Jake Williams (Malachi Lavelle-Moore 79), Joe Burgess (Josh Green 46), Joe Maguire, Courtney Wildin; Herve Pepe-Ngoma, Lewis Hilliard (Grant Roberts 46); Liam Adams (Marcus Marshall 46), Callum Chippendale (Waide Fairhurst 46), Cameron Johnson (Jay Rollins 46); Andrew Ofosu (Lamin Colley 46).
Referee: Josh Smith.
Attendance: 701 (247 visitors).