Curry's better than an average defender. The numbers bear out that he is one of the best one on one defenders at guard in the league. Thompson is good as well.
Some old narratives have a hard time dying.
Hey, an NBA post! How did it take me this long to see it??
You actually understate Thompson as a defender. He's probably in the top 5 to 10 wing defenders in the league. He's elite. But anyone who thinks that Golden State doesn't have wing defenders who can slow down Jordan is nuts. Their entire team is pretty much built around defending wings better than any team in recent memory. Curry's good, Thompson's elite, Iguodala was the MVP of last year's finals mostly because he played absolutely unreal defense on LeBron, Livingston is good, and their bigs, specifically Barnes and Green, can all switch onto wings and more than hold their own--Green's probably the best on ball defender in the league. Now, might Jordan drop 50 on them? Sure, cause he's Michael @#$@@# Jordan! But Golden State would make it hella difficult.
And here's the thing about the larger conversations. Too me, it's a really difficult question that almost can't be answered because both teams were built, both offensively and defensively for their eras. People talk about Jordan averaging 50 a game today, and they fail to realize that in many ways, defenses today have unique advantages that they didn't in the mid-90's. Scoring (on both a raw and points-per-possession basis) since they got rid of hand-checking is actually DOWN significantly compared to the mid-90's. This is not because the players got worse, but rather because the rules committed simultaneously got rid of the old illegal defense rules. Now, teams like the Garnett-era Celtics, Thibodeau-era Bulls, and the Lebron-era Heat are able to play a sort of hybrid switching defense that can stifle the pick and roll and double the post without simultaneously giving up wide-open threes every time. Today's Warriors do all that the above teams did and also add the ability to switch every pick 1-4 (and 1-5 when Green plays center). The thing about the Curry/Green pick and roll (and Thompson to a degree) is that he is the perfect antidote to the new NBA defenses, he will absolutely shoot dribbling around a pick 30 feet from the basket if the big man is not hedging hard. And if he hedges hard, he will simply pass to Green who will play 4 on 3 with deadly precision. Switch the pick and watch Curry destroy every big in the NBA off the dribble. Essentially the Bulls just don't have enough shooting and nimble enough Big men to score and play defense against the Warriors.
But the Warriors would have a really tough time with 90's era rules. Grab Curry every time he goes around a pick and your life gets so much easier. And how would Barnes (and even Bogut?) survive in the post without the ability of help-side defenders to come in waves and then rotate as the ball gets kicked out? Not especially well (although I'm not sure the Bulls have the post players to really take advantage --except for Jordan, I guess). And similarly, without the ability to help on drives nearly as effectively, how would they stop Jordan and Pippin? It'd be really tough.
Anyhow, tl;dr. These teams were designed and built specifically to take advantage of the rules they played under. Asking which one would win is almost like trying to compare a team from now to a team in the year 2045, when they finally capitulate to fan desires and add a second ball.
