For both the regular season and playoffs, I looked at two factors: win-loss record and average scoring margin. Every regular-season win was worth two points, with the 1999 participants having their wins prorated to an 82-game season. Similarly, every playoff win was worth four points, but each playoff loss docked a team four points -- this helped differentiate between champions who went 15-2 (like the 1991 Bulls) and those who went 15-9 (like the 1988 Lakers).
For scoring margin, I took the team's season scoring margin and divided by 15; basically, a one-point-per-game increase was worth 5.47 points in this formula. For playoff scoring margin, I did the same thing but multiplied by four -- since most teams played about four times as many regular-season games as playoff games, this made the two virtually equal.
Finally, I added 15 points to the score of each team that won a championship. Why 15? First, because that amount meant that every champion rated ahead of the runner-up from the same season, and second, because the valuation seemed about right -- the same as 7.5 regular-season wins.
From there, only one other tweak was necessary: adjusting for those teams in the earlier years that didn't have as many early-round playoff games in which to rack up points. Teams that didn't play a first-round series got 12 extra points; teams that played a best-of-three got six points; teams that played a best-of-five got three points. That's an approximation, obviously, but it mirrored what other teams in their situation actually did.