Both Juve and Milan could have won even more Champions League titles in the 90s, they both lost multiple finals in the decade. Milan were generally the best team in Europe from early to mid 90s, and Juve were generally the best team from the mid to late 90s. I imagine that Juve would have been the heavy favourites to win both the 1997 and 1998 finals.
As weird as it may sound, it can be argued that 'only' 3 Champions League titles for Serie A clubs in the 90s, when the league was by far the strongest in the world with none of the Premier League, La Liga and Bundesliga coming close, was actually an underachievement for the league. Of course though their clubs utterly dominated the UEFA Cup in that decade, and also won a few Cup Winners' Cups.