Fresh from Saturday’s resounding 3-0 victory over Bishop’s Stortford, United bagged another valuable three-point haul against Darlington in midweek.
Andrew Nelson was guilty of missing early chances for the Quakers and Mooney on 23 minutes and Knowles in the 65th minute took full advantage.
Darlington manager Steve Watson made unwanted Jakemans Community Stadium history in the process - losing his third visit with three different clubs, following previous stints in charge of York City and Chester FC.
Watson's misfortune was exemplified by Nelson's profligacy in front of goal. The Darlo number 11 was denied by an Aaron Chapman save when clean through, before curling an effort on to the roof of the net from Matty Cornish's right-wing cross.
Moments later, United edged in front when Knowles surged away from a fouling Cardo Siddik, with referee Lewis Dawson playing a fine advantage, and MOONEY tapped the loose ball home from close-range.
Darlington were presented with a decent chance to equalise six minutes before the break, but Nelson failed to steer home Cedric Main's cross to the back post. Chapman made a further save from Cornish at the end of the half.
United were much more in control after the break, with Matty Young saving well from Knowles, following a quick Deji Sotona free-kick. Mooney's header then flew wide from a Sotona corner.
Mooney won the flick for KNOWLES to run on, check back inside and stroke home the Pilgrims' second goal just before the mid-point of the half - to firmly take the wind out of Darlington's sails.
United saw out the remainder of the contest with relative ease - as the home side's play-off hopes were boosted and Darlington's relegation worries increased.
Boston (4-4-2): Aaron Chapman; Jai Rowe, Michael Bostwick, Tom Leak, Ethan Sephton; Michael Gyasi (Dylan Hill 46), Jordan Richards, Zak Mills, Deji Sotona (Keaton Ward 64); Kelsey Mooney, Jimmy Knowles (Adam Marriott 73). Subs (not used): Brad Nicholson, Sam Smart.
Darlington (4-4-2): Matty Young; Ben Hedley, Toby Lees, Cardo Siddik (Kallum Griffiths 52), Scott Barrow; Matty Cornish, Will Hatfield, Tom Platt (Ben Liddle 63), Jarret Rivers; Cedric Main, Andrew Nelson (Mitchell Curry 59). Subs (not used): Cameron Salkeld, Hayden Lindley.
Referee: Lewis Dawson.
Attendance: 1,410 (82 visitors).
PIC: Russell Dossett.