The Bundesliga outfit last week announced that the former Barcelona boss will take charge of the club from the beginning of next season.
However, current chief Heynckes believes that the news has come at a disrupting time for the league leaders.
"It would have been better to do this in the winter break," said Heynckes.
"Before Christmas, before the holidays. This is due to the media hype that might interfere with the normal working day.
"I am the boss. Anyone who knows me knows I am the boss here. I have been the boss everywhere, no matter where I have worked."
Bayern are nine points clear at the top of the Bundesliga.