What would you describe as today's NBA? The entire decade?
Whatever it is, Jordan would have it tough simply because the generation is far more advanced in terms on athleticism, injury support, and general technology to assist the athlete. But that alone does not make a team better.
First off, Jordan's team had two different generations. One was more focused on the frontcourt and the second had more in general. The first generation didn't have guys playing at a high level, but the second generation simply had more firepower.
Taking a look at the teams of this generation, I could make a case for the Mid 2000 Spurs, Early 2000 Lakers, but that's it.
Phil Jackson was still an outstanding coach who could take Popovich to school any day. And what's better than battling yourself? Jordan and Bryant were good, but Jordan was so much better with Pippen, negating Shaq to an extent. That is the limit. LeBron's good, but lacks a strong dynasty to compete at Jordan's level. Kobe had a dynasty, but had to reboot the system before he could get back there, and by then it was too late. Shaq is probably one of the few to really compete with Jordan, but he's not always in shape, taking away many of the advantages.
I think the Bulls are still good, but the new era makes it harder, though not impossible to win 6 championships.