I was a Bulls fan when Jordan played and I agree that Phil Jackson is one of the best coaches to ever coach in the NBA, but look who he had to work with? He had Jordan and Pippen in Chicago, then he had Shaq and Kobe in L.A. He had 4 of the best players to ever play the game. Yes he still had to coach these players to play how he wanted them to play, but if you're talking about best coach in the history of the NBA, there are others that come to mind for me.
Some other names that I would consider are Gregg Popovich, Red Auerbach, Pat Riley, Chuck Daly, etc. If I had to pick one, I'm going with Popovich. The Spurs have been succesful year in and year out the entire time he's been there, and through so many different players. Yeah he had Tim Duncan for many years, but I'd still give the nod to him, ever so slightly.
Here's a good site I found that compares all the top coaches, it's pretty interesting to see some of the other names on the list: