Mark Gray's 16th minute header and Liam King's 85th minute drive handed the hosts all three points and their third victory of the season over the Pilgrims.
It was very much a game of two halves for the Pilgrims, who showed a marked improvement after the break following a sub-standard first half display.
United boss Dennis Greene had opted to deploy three strikers in a 4-3-3 formation, but once Mark Jones had blasted just wide after two minutes, Ferriby bossed the first half.
A fabulous last-ditch challenge from Scott Garner was required to thwart Jason St Juste who was preparing to pull the trigger following a swift Ferriby break, although the visitors' respite was short-lived.
Louis Bruce and Adam Bolder worked a crossing opportunity from the right and the latter whipped in a ball which was powered home by the head of GRAY.
Gray narrowly cleared the Boston bar with another firm header following St Juste's cross.
United introduced wingers Jamie McGhee and Kaine Felix at half-time and McGhee's near post drive was soon tipped wide by Adam Nicklin.
The Ferriby keeper made another crucial save to deny Garner who had reacted to fire goalwards on the end of Rene Steer's cross.
Another massive chance presented itself for Boston with Garner intercepting Bruce's underhit backpass to round Nicklin and fire into the side-netting.
Chances were at a premium thereafter until Ferriby sealed the points with five minutes to play, with the Pilgrims caught cold at the back and KING running on to roll the ball past Joel Dixon from 18 yards.
North Ferriby (4-4-2): Adam Nicklin; Louis Bruce (Nathan Peat 81), Gregg Anderson, Mark Gray, Josh Wilde; Adam Bolder (Jonathan D'Laryea 79), Russell Fry, Liam King, Jason St Juste; Tom Denton, Ryan Kendall (Nathan Jarman 73). Subs (not used): Tim Taylor, Tom Nicholson (gk).
Boston (4-3-3): Joel Dixon; Liam Marrs, Scott Garner, Carl Piergianni, Rene Steer; Zak Mills, Michael Hollingsworth (Ollie Price 87), Conor Marshall (Kaine Felix 46); Dayle Southwell, Mark Jones, Marc Newsham (Jamie McGhee 46). Subs (not used): Louis Saebe, Sam Vince (gk).
Referee: Sam Purkiss.
Attendance: 389.
PIC: Eric Brown.