I don't think Real Madrid is in a good situation right now, they nearly lost the La Liga title to Barcelona and there is o hope for them anymore and this can have a negative effect on the team, however, they have enough time to recover. On the other hand, Bayern Munich started working with a new coach and we can't be sure how they are going to perform even in Bundesliga also he needs some time with his team. While Napoli got a more stable situation.
I don't see league performance and Champions League performance in the same way. Real Madrid always do well in the Champions League. Although they are on the verge of losing the league title but I believe Real Madrid will surprise again in the Champions League. Moreover, Bayern Munich and Manchester City are far ahead in the race to win the Champions League.