City opened the campaign by winning the Community Shield, with a quarter-final Champions League exit to Tottenham their only failure in a history-making year in which they achieved a feat never previously completed by an English club.
"[It is] one of the best seasons I have experienced as a manager. I wouldn't say the best but one of them for sure," Guardiola told a news conference.
"Playing all competitions and after what incredible teams have done in this country to be the first - it means if one team is able then one will repeat sooner or later but we are first.
"I love the Champions League but to do that is more difficult than to win the Champions League.
"For the organisation and [City owner] Sheikh Mansour and these players deserve all the big, big compliments. Because it's not easy, to play every three days - after a bad night you're out.
"Today we played with a lack of energy, winning the Premier League was so tough. This week we could not keep the energy but we had it when we needed it."
Guardiola insisted City can get even better and hinted he will enter the transfer market to add further depth to his squad.
"Individual attributes and moments, mistakes some are repeated in some players they have to improve, maybe a few are coming to help with the way we play," Guardiola added.
"We cannot forget we won the Premier League by one point from Liverpool, we are not far away.
"I said yesterday Liverpool showed how tough it will be, the standard we face, we tried to improve but always in game you can improve, saying that I am more than satisfied of course."
City have been repeatedly linked with Atletico Madrid's Rodri, who is seen as a long-term replacement for Fernandinho, whose season has been affected by injury.