The Pilgrims had more experience in their side, with veteran Stuart Balmer in defence.
Former Town 'keeper Steve Croudson kept goal for the home side but he couldn't prevent Nick Heggarty or Liam Nimmo scoring the Mariners' goals. Former Lincoln striker Dene Cropper got the consolation goal.
Boston also fielded Bradford and former Manchester United midfielder Ben Muirhead as he tries to impress for a contract at York Street.
Town: Fraser, Smith, Howard, Chamberlain, Webb, Wheeler, Hildred, Ashton, Nimmo, Lightowler, Parker(L). Subs: Heggarty, Stares, Newton.