Germany captain Neuer and positional rival Ter Stegen were locked in a public exchange in the lead-up to this week's Champions League matches after the latter ended the international break unhappy with being overlooked for a pair Euro 2020 qualifiers.
Neuer, 33, suggested his international team-mate was putting himself before the team, criticism which Ter Stegen described as 'inappropriate'.
The tension seemed to be easing until Hoeness hit out at Ter Stegen following Bayern's routine 3-0 Champions League win over Red Star Belgrade on Wednesday.
Hoeness accused sections of the German media of treating the 27-year-old as if he had won the World Cup '17 times' and insisted Neuer was the 'much better' goalkeeper.
Though appreciative of his president's backing, Neuer refrained from adding to the sense of disharmony between himself and his fellow countryman.
"It's always good to have some people support you in general," the Bayern skipper said when asked about Hoeness' comments.
"I basically said one thing about it because I got asked after a game.
"I don't want to have a debate and talk about who can do what better than the other. We are a team and I am a team player. We know that we have four good goalkeepers who play together and do everything for Germany.
"So, I don't want to talk about it anymore."
Hoeness' tirade involved a shot at the German Football Association for a perceived failure to adequately support Bayern players.
Earlier this year, Germany boss Joachim Low made the sudden decision to move forward without 2014 World Cup winners Thomas Muller, Jerome Boateng and Mats Hummels, who has since moved to Borussia Dortmund.
Neuer remains firmly in Low's plans and recently won his 90th cap international cap, 68 more than Barca star Ter Stegen.
Bayern return to action this weekend with a Bundesliga clash at home to Koln, while Arsenal, who sit seventh in the English top-flight, will take on Aston Villa in the Premier League a day later on Sunday.