Wilder, 51, led United to second place in the Championship behind Norwich City, whose German manager Daniel Farke was also on the shortlist, to earn promotion to the Premier League.
Former Manchester United manager Alex Ferguson and England coach Gareth Southgate presented the award on behalf of the LMA at an awards dinner.
Guardiola was named Premier League manager of the year after City finished a point above Liverpool to retain the title.
Klopp and fellow Champions League finalist Mauricio Pochettino of Tottenham Hotspur plus Wolverhampton Wanderers' Nuno Espirito Santo were also short-listed for that award.
Spurs' Karen Hills won the Women's Championship award after steering the London club into the top tier, while Arsenal's Joe Montemurro took the Super League prize after winning the title.
(Writing by Ken Ferris; Editing by Nick Mulvenney)
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