I would rate it like this:
1. Treble team (97-2001)
2. 06-09 United
3. Pep's City
4. Chelsea 04-06
5. Arsenals Invincibles (01-05)
I will start by saying that the invincibles are overrated.Never at any point were they considered the best in the world like the others had been, in addition, their success was not sustained, and their inability to match european performances to league performances highlighted the limitations of the team. At this level, we are dealing with the best teams in league history, so even slight issues have to be highlighted. That Arsenal team could not dominate even the third or fourth placed teams of other leagues at the time. They were usually beaten away from home, and had issues of inconsistency in Europe. In the premier league, they could get away with this because of the difference in class between them and the other teams in the league outside the top three, however in europe, their actually class value became more obvious. In addition they did not have as much depth as any of the other great teams or as good a right hand side ( which is big enough to create a deviation as the other teams have near perfect starting 11s). In addition, Chelsea usurped them a year later, quite easily and with more success on both domestic and european fronts.
The Chelsea team during Mourinho's run were dominant and much better than their competitors in the same way utd's treble and pep's city have been. They benefited, like the invincibles, from facing a rebuilding manchester united, and were never truly the best team in the world despite their domestic dominance, as Milan, Juventus and Barcelona had better claims to that throne. In addition, the 06-09 utd side usurped them despite the fact that most of the squad of the 04-06 run were still in their prime.
Pep's city has won everything domestically and has done so in a dominant manner. In addition, the strength of the league has risen quickly in the two seasons they have dominated, which makes it more impressive, as the league is now stronger than at any point outside of the 2006-2011 teams. However, they have not been successful in europe, and have usually been beaten by teams from the EPL when eliminated. I believe they have the most depth amongst all the teams, but also a much inferior defence, which has been protected by probably the most dominant midfield of any of the teams. I believe in a one off game they would handily beat Arsenal's invincible's as their possession football would inspire the same difficulties arsenal had in the champions league during that era, but would lose to the other 3 teams. I feel they would have won the league against all the teams except from the 2008 team, since that team could almost match their depth. The treble and 06-09 teams were dominant against the top sides of their era whilst also dominating their leagues. Despite me thinking city are the best team in the world, they have yet to show it against any other contenders for the throne besides liverpool, maybe they will soon, but as of now, they have not.