The Manchester United boss believes victory at Wembley on May 11 would be a fitting reward for Whelan, who bought the club in 1995.
Since then, under Whelan's ownership, Wigan have reached the final of the League Cup and have been a Premier League club since August 2005.
Even if Wigan fail to beat Manchester City in the capital, they are still likely to play in next season's Europa League - providing the Citizens remain on course for a Champions League spot.
And Ferguson said: "I hope Wigan win the cup and not because it would be at the expense of Manchester City.
"In Dave Whelan they have an owner who has not only shown great faith in his manager but someone who invests so much emotionally in his club.
"People like Dave Whelan deserve the kind of reward that a Wembley win would provide."
The 76-year-old Whelan is a former professional footballer who played for Blackburn in the 1960 FA Cup final where he was stretchered off the Wembley turf with a badly broken leg sustained after 43 minutes of the defeat by Wolverhampton Wanderers.