I'm going to cheat and add "or on television" to the question.
In my mind, it comes down to '69 versus '86 versus '94.
The '69 team was dominant on D, with five All-Americans (to include Honorable Mentions), undefeated, and totally throttled the then Big-8 champ in the Orange Bowl.
The '94 team featured one of the best offenses in the history of college football, went undefeated, with only two games being relatively close (Michigan and Illinois).
But I go with '86, which might have been Joe's favorite team based on a couple quotes of his. Wonderful, tough trademark defense and teamwork. Undefeated. National champs. And of all three of the mentioned squads, the '86 group won the biggest game of all against the toughest team of all.
It was the high point of Joe's career, but we didn't realize it at the time. I've watched the replay a number of times...and still love Bob Griese's line after, like, the 4th Penn State interception: Vinnie's seeing linebackers where there aren't any. Vinnie probably still sees them to this day.