Allen, 28, marked her return last November with "Hard Out Here", a song and accompanying video attacking “body image pressures and misogyny in the entertainment industry”.
Her cover of Keane's “Somewhere Only We Know”, accompanying the John Lewis Christmas advert, topped the charts.
The re-emergence of one of pop’s most outspoken artists was rewarded by readers of the weekly music title in a highly competitive category.
Allen, who also presented Debbie Harry and Blondie with the Godlike Genius award at the O2 Brixton Academy event, said she had retreated from showbusiness in 2011 after finding herself surrounded by “sterile f***ing botoxed idiots”.
Arctic Monkeys added five NME Awards to their double win at last week’s Brit awards. The Sheffield band’s haul included the Best British Group, Album and Live act honours.
Drenge, the garage-blues duo namechecked by Labour MP Tom Watson in his shadow cabinet resignation speech, were voted Best New Band. Watson underwent an epiphany when he saw the band play at Glastonbury.
The Derbyshire band - comprising brothers Eoin and Rory Loveless - said they were “not totally overjoyed” at the talent-spotting MP’s endorsement.
Haim, the California band formed by three Californian sisters, struck another blow for siblings after beating Arcade Fire and Vampire Weekend to the Best International Group award.
Damon Albarn, set to release his first solo album, took the NME Award For Innovation. Sir Paul McCartney was presented with the Songwriters’ Songwriter Award, 51 years after The Beatles performed second on the bill to Cliff Richard at the NME Poll Winners’ All-Star Concert at Wembley.
Fat White Family, an independent label band who have offered to cook dinner for any fans who will help fund a trip to play at the SXSW festival in Austin, Texas next month, were given the Philip Hall Radar Award, traditionally presented to an act to watch.
NME’s weekly print sales fell below 20,000 this year, with the 62 year-old publication unable to buck a decline across music magazines.
A perceived dearth of great, new British guitar bands may have exacerbated its decline.
However, the NME website gets 1.4m users per week, while the digital edition of the magazine sells 1,307 copies a week, and thousands of people attend NME live events and concert tours.
One Direction were relieved of the Worst Band award by The 1975, the slick pop-rock quartet from Manchester, whose self-titled debut album topped the charts. Harry Styles, however, won the Villain of the Year vote ahead of David Cameron.
Johnny Marr presented Arctic Monkeys with their Best British Band prize but was not invited to pick up the award for his absent former Smiths colleague.