Hard to tell which team is the best. Both had set records in their season. And last season was special because of Corona.
The 2013 team was more balanced, but I'll still go with the 2020 team. Why? Because it was more fun!
For a Bayern fan, the whole last season felt like a movie. A painfully bad start with Niko Kovac, leading to a disastrous 5:1 loss in Frankfurt and up to 9 points behind Dortmund. Kovac was fired, Flick would lead the team until the end of the season.
His first two games he won 4:0 (the first against Dortmund), football was fun again! ... and the next two games he lost 2:1 to Leverkusen and Gladbach. I think many Bayern fans at that point were just waiting for the new season to start, with a new coach (the one from Ajax was in pole position).
Nobody could have imagined that this team would beat every team (except the 0:0 vs Leipzig) until the end of the season! Most of them with ease, even the bigger teams. Ok, the final against PSG was a close one, but still.
Thing is, nobody was really surprised when Bayern won it 2013. After two lost finals in 3 years, it was overdue.
2020? This team was a mess. I remember reading the predictions after the start of the season, and not even Bayern fans were expecting this. Only Lewa said something like "I still believe we can do this!". We laughed at him, but he was right!
Flick has done a tremendous job in forming a mediocre team into a dominating CL winning team - in only a few months!
How Arsenal won that second game nobody knows, they had 2 shots and scored 2 goals.
I remember Schweinsteiger not playing (because of yellow cards I think?) and he was a big loss back then. In my opinion he was in his prime in 2013 and 2014, winnig the CL and the WC as the leader of both teams. Yes, I know Lahm was the captain, but I think everyone knows who the true leader was back then.