The '03,'04, and '05 Spurs were all better than '99 AND this year's Miami team. The '99 team didn't have Bruce Bowen - don't underestimate how good he was on the perimeter.
Don't let the .4 shot re-write history for you. In 2004, the Spurs limited their opponents to just 84.3 PPG. (And that wasn't a lockout season.) That was an incredible defensive team, regardless of losing the series to the Lakers. Had the Finals matchup that year been between the Pistons and Spurs, it would have been the epic defensive battle of all time.
For that matter, the Pistons who won the Championship that year ('04) were a better defensive team than Miami is this year. That's not to take away from Miami - it's just fact.