The 67-year-old feels Diego Simeone's side should be the ones to win the Spanish top flight, but Hristo Stoichkov has tipped the Blaugrana to retain their title
Atletico currently sit three points ahead of Barca, who they meet on the final day of the season, and a further point ahead of Real Madrid with two games left to play.
Cruyff believes Diego Simeone's men, who will meet their city rivals in the Champions League final, merit the title, although he says that even if they stumble their campaign must still be regarded as excellent.
"Atletico Madrid deserve the title more and if they lose it, which could happen, they’ll have had an exceptional season anyway," he told reporters.
Meanwhile, failure to win the league would be a huge disappointment for Barcelona after they crashed out of the Champions League quarter-finals at the hands of Atletico and lost in the Copa del Rey final to Real, and the former Barca star feels it is the board's fault as they do not understand football.
"The decisions are taken by those at the top and that makes it difficult for things to turn out well, because those at the top don’t know about football," he said.
"The end of an era is only an excuse when you don’t know what isn’t working. Normally, if you know about football, you should know why this worked before and doesn’t now."
The 67-year-old added: "I don’t think Real Madrid are going to win all three trophies."
On the other hand, Stoichkov predicted that the Catalan side will emerge victorious in La Liga while the Rojiblancos will beat Carlo Ancelotti's men in the Champions League.
"It reminds me of the title that Deportivo lost at the Riazor [in 1994]. We were dependent on Deportivo not winning and, in this instance, Barca will be champions if they win their two games.
"Anything can happen, that’s true; but I fancy Barca to win the league and Atletico the Champions League. Madrid have the Copa del Rey. Not long ago, Madrid thought that they were going to win the treble, but that’s not going to happen.
"You can’t give the impression that you’ve lost the league after two slip-ups, because football is full of surprises and in two days the statistics have been in favour of three different teams."