While United have struggled since Ferguson departed in 2013 – failing to win the Premier League – Bayern continue to dominate the Bundesliga with seven successive titles.
United finished sixth in 2018-19 as they missed out on Champions League qualification, while the Red Devils are still searching for a director of football to assist manager Ole Gunnar Solskjaer.
And Ferguson hailed Bayern's hierarchy, which is led by president Uli Hoeness and chairman Karl-Heinz Rummenigge.
"They're a great club. It's a club run in the proper foundation of it," Ferguson told MUTV prior to Sunday's Treble Reunion game, which United won 5-0 at Old Trafford.
"Former players who run it really, Uli Hoeness and Karl-Heinz Rummenigge, they run the club in the right way and they are always winning the league in Germany. They're a great club."
Solskjaer and United are facing a big off-season after finishing 32 points adrift of rivals and champions Manchester City.
Ander Herrera and Antonio Valencia have already announced their departures, while there is uncertainty over Paul Pogba, David de Gea, Romelu Lukaku, Juan Mata and Alexis Sanchez.
Jaap Stam, who won three consecutive Premier League trophies in three years in Manchester, said Solskjaer has to make some "hard decisions" in his quest to restore glory.
"I think we definitely could do with some more quality up front, in midfield and the back four as well," Stam told Sky Sports News.
"You want a squad that is competitive towards each other. Everyone needs to push each other to get the maximum out of everyone - to achieve something.
"As manager and as a club you need to have a look at that. After the last couple of seasons and how everything is going, I think it is good to re-evaluate everything in the team.
"Look at the players, what they have done and what they have achieved. Even players who have a contract for another three or four seasons - you need to make your choices towards them and what you want to do with them.
"At the end of the day the most important thing is to achieve the goals you set out, sometimes you need to make hard decisions to do that."