Howe confirmed last week that the 25-year-old picked up a foot injury, while he was also dealing with an eye issue that forced him off at half time in a 2-1 win at Wolverhampton Wanderers.
However, Isak received a pain-killing injection to start and play the full 90 minutes in Newcastle's 3-1 defeat against Fulham at Craven Cottage last weekend.
The Magpies squad have been blessed with a few extra days rest this week after their EFL Cup third-round tie against AFC Wimbledon on Tuesday was postponed as "extensive overnight flooding" created a sinkhole on the pitch at the Cherry Red Records Stadium.
Isak would presumably have been rested in that match anyway, with one eye on Saturday's tricky top-flight clash with Man City, but Howe has now revealed that the Sweden international is yet to take part in training this week due to a toe injury.
Howe delivers update on Isak, Targett
Speaking at a pre-match press conference on Friday, Howe said: "In terms of fresh injuries, Alex is still nursing his toe injury and will be a doubt for tomorrow. He hasn't trained yet so we will have to make a decision on him."
Meanwhile, Howe is hopeful that Matt Targett will return to training on Friday, but the defender will not feature on Saturday due to "a flare-up of eczema".
"We don't have anyone coming back that has been out. Matt has had a flare-up of eczema so he's been nursing that over the last couple of weeks," Howe added.
"We are hoping to get him back training today but he won't be involved in the game (against Man City)."
Newcastle will also be without striker Callum Wilson (back), midfielder Lewis Miley (ankle) and defensive duo Sven Botman and Jamaal Lascelles (both knee) due to injury.
Who could replace doubtful Isak in attack?
Newcastle are already light in the centre-forward department with Wilson on the sidelines, and if Isak fails to pass a late fitness test, Howe could turn to one of two options.
Summer signing Will Osula is the only other recognised striker in Newcastle's first-team squad and has struggled for game time since joining the club from Sheffield United for £15m.
The 21-year-old made his Magpies debut when he came on for the final seven minutes of the loss to Fulham, having previously watched on as an unused substitute in the club's first five matches in all competitions.
Howe's other attacking option who could play centrally is Anthony Gordon, who played down the middle for the second half of the win at Wolves when Isak was withdrawn at the interval.
Like Isak, Gordon has scored just one goal across five league games so far this season, and it is Harvey Barnes who tops the Newcastle scoring charts thus far with three goals.
Newcastle lost both home and away against Man City in the Premier League last season, but they did secure a slender 1-0 home win over the Citizens in the EFL Cup third round this time last year, courtesy of a second-half strike from Isak.