Panel chairman Chris Kamara said: "This is the fittest I have ever seen Dean, He's worked really hard in pre-season and this definitely showed.
"There is no reason why he cannot go on and better his best ever goals tally."
Windass was the the subject of a transfer approach from Premiership new boys Wigan before the transfer window slammed shut.
But he has also courted controversy, with the Football Association looking into claims he has biten rivals players.
Huddersfield's Pawel Abbott, Rotherham's Deon Burton and Swansea's Roberto Martinez were also nominated.
Wycombe's Nathan Tyson took the League Two prize, with Wolves defender Joleon Lescott taking the honours for the Championship.