Manchester United finished second in the Premier League – a staggering 19 points off rivals City.
But despite the noisy neighbours racking up a record 100 points, Neville thinks Mourinho can overtake Guardiola as the city's best boss.
He told the Daily Mail: "These two managers have been at Real Madrid and Barcelona and both won leagues there.
"Ultimately at the end of next season if Pep wins another league that will be a big problem over a three year period.
"But if Jose was to win the league next year you could actually argue Jose has done the better job. Next season will be critical."
Mourinho has been heavily criticised for his style of play as well as results on the field.
But Neville thinks the Special One is being unfairly singled out – insisting the football was not always brilliant under Sir Alex Ferguson.
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He added: "Under David Moyes, Louis van Gaal and Jose Mourinho it’s been suggested the football is not very good.
"I think we’ve become a bit idealistic about what the football was at times under Sir Alex. I was there for a large part of it, 21 years, and saw every game.
"Yes, it was mesmerising at times, but from 2003 to 2006 it wasn’t good. I played in that team, it wasn’t good. We weren’t playing at a high level. We were pretty average.
"So you think about this three-year period or so now and what are you measuring against?
"Sir Alex’s 1999, or the 2003-2006 period when the football was pretty poor and Jose Mourinho was at Chelsea and destroying us?"
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