Of course you'd be happier facing Boston, they're older and their style of play matches the Bulls. Miami isn't on another planet from Chicago. Both teams are right there. 2-1 regular season series doesn't really matter (albiet from last year)... Chicago was 3-0 against Miami last year in the regular season and ended up losing that series in the playoffs in 5 games. The playoffs are different. It's all a half court game. If the Bulls were able to stay with Miami's offense last season (in 2 or 3 of the 5 games), then they can sure as hell handle NYs offense. Neither Chicago nor Miami is worried about NY at this point and I don't think they will be either, the biggest threat to each of those teams is a each other in a 7 game series. Right now, if Miami and Chicago were both a full strength, I can't pick an east team that I'd say would have a chance against either in a 7 game series.
You're right about the other stuff, but the Knicks have been playing pretty good defense this year. They are 8th in defense efficiency, which while not on the level of the Bulls, are pretty good.