Cropper broke the deadlock against Braintree Town two minutes before the hour mark - with Hill wrapping up maximum spoils with United's second goal three minutes in stoppage time.
Rhys Lovett had laid the platform for Hill's clinching strike with a magnificent save to deny Frankie Terry two minutes earlier.
Rocco Coyle, Kieren Donnelly and Lenell John-Lewis were the three players coming into the starting XI ahead of kick-off, as the Pilgrims chased a third successive win against Braintree since promotion back to the National League.
Boston started brightly territorially, but Braintree had the better early chances with James Vennings crashing one effort wide and Tom Blackwell forcing Lovett into a smart save.
United crafted a glorious chance in the 25th minute with Cropper digging out a cross from the right, with Donnelly only able to steer a bouncing ball wide.
The Pilgrims edged in front 13 minutes after half-time, with CROPPER rifling home a low drive from the edge of the area which left Town keeper Mason Terry with no chance.
Lovett produced a huge save in the first minute of stoppage time to claw aside Frankie Terry's header - with United taking full advantage to go up the other end for HILL to roll the ball home at the second attempt and clinch the win.
Boston (4-3-1-2): Rhys Lovett; Jordan Cropper (Ben Grist 89), Connor Teale, Zak Mills, Matty Carson (Alex Lankshear 74); Rocco Coyle (Owen Hampson 74), Jordan Richards, Greg Sloggett; Dylan Hill; Lenell John-Lewis (Jordy Hiwula 83), Kieren Donnelly (Tommy Fogarty 89). Subs (not used): Manni Norkett, Bobby Jones (gk).
Braintree (4-2-3-1): Mason Terry; Jacob Pinnington, George Langston, Aidan Francis-Clarke, Frankie Terry; Marley Marshall-Miranda, James Vennings; Chay Cooper, Goran Babic (John Akinde 78), Terrell Works (Olly Davis 83); Tom Blackwell (Regan Clayton 74). Subs (not used): Manny Omrore, Sahid Kamara, Freddie Hockey, Elliot Thorpe.
Referee: Jamie O'Connor.
Attendance: 1,356 (46 visitors).
PIC: Chris Bray.