The Premier League champions received the honour after delivering "stand-out customer experience" for their United fans.
A panel of experts identified the Old Trafford club as the best place to watch football last season.
But David Moyes and co were not the only big winners. Wigan Athletic, relegated from the Premier League last term, received the Unsung Hero award for the work by steward Jo Roberts helping disabled supporters at the DW Stadium.
United's arch rivals Liverpool picked up the Best Fan Innovation accolade for their Family Park at Anfield.
And Fulham won an award for Warmest Welcome for their steward's work at Craven Cottage.
Last year marked the first time the awards were presented, with Arsenal, Fulham, Liverpool and Manchester City scooping the top prizes in 2012.
Arsenal took the Club of the Year title last term, while Liverpool were awarded the Warmest Welcome for their steward's efforts at Anfield.