Neave's impressive 24-minute treble fired the young Magpies into a commanding lead at the Jakemans Community Stadium, with the 18-year-old striker opening the scoring from the penalty spot before netting two impressive finishes in the space of ten minutes before the break.
Frankie Maguire's dipping effort after the restart pulled a goal back for the National League outfit, who had won three successive Group D fixtures prior to facing United's second-string, but the goal would prove a consolation as Newcastle's youngsters continued their 100 per cent winning start in the competition.
Adam Lawrence made five changes from Sunday's 4-1 defeat against Tottenham Hotspur in the Premier League 2 as Neave, who was named on the bench for the Magpies' Carabao Cup final victory against Liverpool, returned from a one-match suspension while Seung-soo Park, who made his full United debut during a pre-season friendly against RCD Espanyol at St. James' Park, was also named in the starting line-up.
Miodrag Pivaš, who joined the Magpies from Serbian SuperLiga side FK Jedinstvo Ub in July 2024, prevented Jordy Hiwula from opening the scoring in the early stages of the Group D clash, with the 20-year-old centre-back blocking the Boston forward's first-time effort out for a corner.
Newcastle took the lead in the 16th minute through Neave's successful spot-kick. After Charlie McArthur completed a dangerous run into the box, the Scotland Under-21 international was tripped inside the box before Neave netted his fifth goal of the season from 12 yards, emphatically drilling his attempt into the bottom left-hand corner via the post.
Magpies skipper Cathal Heffernan completed a terrific last-ditch challenge to turn away Kieren Donnelly's powerful drive out for a corner, who latched onto Michael Kelly's teasing pass in behind the United defence.
Newcastle goalkeeper James Taylor produced two saves in quick succession shortly after as the Kettering-born teenager parried Kelly's strike at goal before quickly blocking Rocco Royle's rebound out for a corner.
The 19-year-old 'keeper was alert for the resulting corner as Kelly's dangerous goal bound header forced Taylor into scooping the ball around the right-hand post.
In the 30th minute, Neave netted his and United's second goal of the night as the Winlaton-born striker raced onto Scott Bailey's pass and after evading a sliding challenge inside the box, placed the ball beyond Boston goalkeeper Bobby Jones.
Neave completed his hat-trick, a first at under-21 level, in the 40th minute as the England Under-18 international raced onto Park's excellent pass before calmly placing a low effort into the bottom right-hand corner, taking his goalscoring tally to seven in his last eight matches at second-string level.
With the half-time whistle nearing, Neave almost netted a fourth in stunning fashion as the confident forward spotted Jones off his line before his audacious lob landed on the roof of the net.
Newcastle's hopes of a first clean sheet of the season were dashed within two minutes of the restart as Boston pulled a goal back through Maguire, who cut inside to evade the challenge of Kacey Wooster before his dipping strike from the edge of the box flew past Taylor.
United were left appealing for a second penalty of the night as Wooster surged onto Neave's pass and, after advancing into the penalty area, saw his effort blocked by the sliding Connor Teale but referee Emily Heaslip waved away the decision.
There was a debut at under-21 level for 16-year-old midfielder Sam Alabi, who captained England at under-17 level last month, in the closing stages as Newcastle produced a steady defensive display to comfortably see out the cup clash.
Newcastle United Under-21s: James Taylor, Ciaran Thompson, Charlie McArthur, Cathal Heffernan (c), Miodrag Pivaš (Joe Brayson 78), Scott Bailey, Alfie Harrison, Anthony Munda, Kacey Wooster, Sean Neave (Sam Alabi 86), Seung-soo Park (Dylan Charlton 70).
Subs not used: Adam Harrison, Logan Watts, Fraser Harper, Mohamed Waddani.