Muller scored with two headers, starting the scoring after 33 minutes and netting again in the 88th after league top scorer Robert Lewandowski bagged his 23rd of the campaign in the 54th.
David Alaba's long-range effort in the 90th minute capped a comfortable evening for the Bavarians.
After 18 games, the Munich side have 42 points with second-placed Leipzig on 35. Leverkusen and Wolfsburg both have 32.
Schalke, struggling to avoid relegation, had the stronger start with a string of chances and Mark Uth missed the best of them with a header from seven metres.
Bayern needed about 20 minutes to find their way into the game and gradually took control, going in front when Joshua Kimmich floated a cross into the box and Mueller scored with a darting header.
Lewandowski then latched onto another superb Kimmich assist to slot the ball home, setting a league record by scoring in an eighth consecutive away game.
The Royal Blues, anchored in last place on seven points, refused to give up and had opportunities before Bayern scored twice through Muller and Alaba in the final four minutes.
The Bavarians have scored a club record 53 goals after 18 league games which is more at this stage than in any season.