United trailed 1-0 at the break, but conceded three times after half-time to round off their home campaign on a losing note against a side managed by ex-Pilgrim Chris Swailes.
Steve Welsh’s side will complete their season with back-to-back away trips to Birmingham City and Harrogate Town on May 8 and 10 respectively.
Boston (4-3-3): Tom Benton; Niall Delahoy, Charlie Melville, Joe Cain, Jordan Sowerby; Aaron Eyett, James Reed, Lewis McKue; Karolis Andriulionis (Brendan Burton 56), Charley Sanders, Leon Squire. Subs (not used): Juris Kormis, Sam Vince (gk).