The Chelsea boss feels the striker has "made the difference" in the Premier League title race, adding he feels the Liverpool star should still be punished for past mistakes
The Liverpool star picked up both the Professional Footballers' Association and Football Writers' Association awards after notching 31 times this season - and a goal against Newcastle will break the 38-game record.
When asked whether he voted for the Uruguayan, the Chelsea manager told reporters: "He bites, not this season, the previous season.
"This is a different season so I'm not speaking about one mistake that a man can have, and you will have to be punished for the rest of your life if you make a mistake on the football pitch so that's not the point for me."
Dzeko has scored 16 times this season, a season-best for him since joining City and Mourinho feels the Bosnian has proved to be highly reliable in light of injuries after starting the season third in the pecking order.
He continued: "My player of the year would be always from the champion, always, so if the champion is Man City. I would say a City player and if I have to choose one, I think I would choose Dzeko.
"Why? Because he was the third striker in the beginning of the season, he was even behind his manager's first choices and when the team needed him, in crucial moments of the season, he made the difference.
"He made the difference, Dzeko. In this moment, I think he has 16 goals. Sixteen goals for the third striker is something spectacular, and not just that, the quality of his game."
In a thinly veiled jibe at Suarez, Mourinho underlined Dzeko's disciplinary record, adding: "So if I would choose, and also the kind of player he is.
"He's not just a goal scorer, he assists, he plays, he behaves, he's fair, he doesn't dive, doesn't try to put opponents on the stands with accumulation of cards. I would choose Dzeko."