The first one being just a pair of players there are terms like alignment, rhythm, harmony, synchronicity, and magic that would seem appropriate.
Teamwork, collaboration, unity, and cohesion would be more appropriate for the second since this is talking about a larger set of players.
If you want a term for both, collaboration would be my suggestion.
As for Matt's suggestions:
Spark could work as, "The spark between Jordan and Pippen helped their team to win the championships for the Chicago Bulls."
X-Factor can be a bit more tricky as each person has part of the recipe here and not all of it since the idea is that these players coming together brought great success.
Rapport would likely require one to have the understanding that this is within the context of playing the game together rather than just having an understanding within communications.
In the second context, another phrase one could use is that, "The whole is more than the sum of the parts," as the idea is that a team with chemistry can do more than what each player could do alone.