Led by Messi's former coach Pep Guardiola, City are sailing at the top of the Premier League with 34 points, eight more than nearest rivals Manchester United, while they have a perfect record in Europe.
PSG are also five wins from five games in the premier club competition and are looking strong at the top of Ligue 1 with Neymar, Edinson Cavani and Kylian Mbappe in attack.
Messi sees those two as the biggest dangers to Barcelona's hopes of winning the Champions League this season.
"City is one of the strongest teams at the moment together with PSG," he told Marca .
"So far, they have been the two teams that have shown themselves to be favourites, but this is a very long and tough competition."
Although Zinedine Zidane's side have won just two of their last five games, Messi expects them to bounce back and make things difficult for his side in the league and Champions League.
"I never rule out Real Madrid because although they're not having the results that everyone expects, I have no doubt that in the end they will be fighting for everything, as they do every year.
"Bayern is another big team that will also be there at the end, but it's true that today City and PSG are the best."
The 30-year-old was awarded the European Golden Shoe on Friday after scoring 37 goals in the league last season and remains at the top of his game,
As an elite athlete, he has to stick to a strict diet, and he admits there is one thing he misses eating.
"Chocolate, it's the hardest thing for me, even now," he said.
"I occasionally sin with chocolate."