Managerial ability is a mixture of two dozen skills at the bare minimum. Objectively speaking I believe Pep was better at a majority of aspects of the coaching job than Heynckes. We played by far the most aesthetically pleasing and dominant football I have ever seen Bayern play during Pep's tenure. However he had one fatal flaw in Munich. He did not trust his players, micro-managed them, his communication skills were lacking and it showed in the big games in April in May. At the same time let's also admit for a moment that his three exits from the CL were not solely caused by his tactics. A player revolt, individual players falling asleep during set-pieces, bad luck, the decline of former world-class players, tons of injuries and a missed penalty kick also played significant roles.
However since most Bayern fans and the front-office are ultimately obsessed with winning the Champions League we'd pick Heynckes because he's the ultimate coach to shape a team for the knock-out stages in April and May. However that doesn't automatically mean he's better than Pep.