The 31-year-old is believed to be on the verge of signing a three-year deal worth $2.1 million with Manly, who need to replace departing captain Daly Cherry-Evans at the end of the season.
Canberra have offered less money and only a two-year deal, which would allow for the development of young playmakers Ethan Sanders, Adam Cook and Ethan Strange.
Stuart was upset that Canberra never got to table their own offer, with Fogarty's manager Tas Bartlett cancelling a weekend meeting due to illness.
The veteran coach said he could understand why Fogarty would take the Sea Eagles' deal but, if it wasn't done, would "love to have him".
"If that (deal) is real - three years at $700,000 - Jamal should take it - I'd love to keep him but we can't match that," Stuart told SEN radio on Thursday.
"Jamal is 32 at the end of the year and if he can get three years and that's real, Jamal's got to take that as all along I've said he has to look after his young family but I would love to have Jamal here for another two years.
"So wow, good on on you, and I'll say that to Jamal when I see him tomorrow.
"If it's done. If it's not done I'd love to have him."
Stuart said he would look to recruit an experienced half should he lose Fogarty, to keep the pressure off his youngsters.
"I will go and look for another experienced half because it is such a big position," he said, ahead of the Raiders' clash with the Dolphins on Sunday in Canberra.
"It's such a lot of pressure on the halves, I've got another young half here in Ethan Sanders, another young half in Adam Cook and another young half in Ethan Strange.
"I will be looking for another player that has the ability to play a couple of positions and/or play halfback, that can help those boys transition and develop in their early part of their career playing NRL."
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