Interesting debate. Let’s try to address all the basic issues of that have been raised throughout the course of this discussion at the same time in order to clear things up a bit.
This decade almost certainly refers to the decade that began in 2000 and will end at the end of this year 2009. Properly speaking, this would not include the 1999 Spurs championship, and thus during this decade the Spurs and the Lakers have an equal number of championships (3).
Yet at the same time, I think it would make sense to refer to “eras” rather than to the artificial temporal constructs that decades represent. We could thus refer to the Kobe and Duncan eras of their respective teams since those are basically the only players that have been with their teams from the “beginning.” From this perspective, Duncan’s Spurs have 4 championships in this era to Kobe’s 3. I think thus that the number of championships is more a less a wash with respect to the question of the best team of the decade or era, nonetheless with an advantage going to the Spurs.
I think that head to head playoff matchups are less important when it comes to the overall question because as Spurs fans have pointed out, the Lakers have missed the playoffs on several occasions when they certainly would have been beaten by the Spurs. In terms of questionable calls that went against either the Spurs or the Lakers, I think that likely should not figure too heavily in favor of either team with respect to the original question.
The Lakers’ 3-peat deserves mention because if only for the fact that the Spurs did not manage a le defense in the decade/era thus far. However, the Spurs do hold the edge in terms of consistent regular season excellence.
In sum, I believe the body of work presented by both teams in this decade/era is fairly similar with a slight edge going to the Spurs for having 1 more championship and more consistent excellence in the Duncan era as opposed to the Kobe era. That said, there still remains one more year in this decade at least and I think that should either the Lakers or Spurs win this year, then that team would decisively demonstrate that they deserve to be called the best team of the decade.