The United full-back netted in the second half at RAF College Cranwell, but the damage had already been done.
It was United's third successive Football Conference Youth Alliance defeat.
Boston (4-3-3): Jamie Bradley; Daniel Worthington (Harry Bunce 46), Miles Lynch, Ollie Price, Jordan Sowerby; Aaron Eyett, Jacob Pease, Corey Newman; Leon Squire (Steven Dovey 46), Liam Moran (Karolis Andriulionis 70), Bradley Easey.