The top three are very close - Ferrari and Red Bull dominated 2001-2004 and 2009-2012 respectively, however McLaren have been the most consistent challenger against the respective winner.
Brawn gets fifth place because of the historical significance of winning the championship in their maiden year and on a shoestring operating budget - even if they did start the year with the most expensive F1 car in the history of the sport thanks for Hondas billions.
Ferrari was much better than McLaren or Red Bull. Ferrari won 5 more titles than Red Bull. Ferrari scored 54.80% of all possible points to score as a one team during this century. McLaren 40.85% (or 42.97% if you add 2007 points). Red Bull 34.48 as a Red Bull and 24.29% as a team since 2001. Renault 26.96% in 2002-2011 as Renault and 25.71% since 2001. BAR/Honda/Brawn/Mercedes makes top 5, close to Williams. 18.14% vs 17.59 for Williams. Brawn was one year wonder so I wouldn't include it as a separate entity. Brawn stats are close to what Ferrari have done since 2001 with 56.21%. To see my list look above at my previous post.