Moore, who helped guide Australia to a final at the 2015 World Cup, suffered a lapse in form at the start of the Super Rugby season after joining the Queensland Reds from the ACT Brumbies.
But Cheika said the 34-year-old veteran had turned the corner.
"Moorey is going to be the captain for sure and he knows, too, there's some stiff competition," Cheika told reporters. "His thing is in-tight, leadership, being aggressive, that's what I want from him.
"I think he's doing that for the Reds, he's being very abrasive in there and getting stuck in."
Western Force hooker Tatafu Polota-Nau and the New South Wales Waratahs' Tolu Latu had also had good seasons to put their hands up for selection, Cheika conceded.
"Moorey knows that, too. Captaincy's a leadership issue whether you're in the team or not," he said.
Flanker Michael Hooper, who has previously captained the Wallabies, has long been seen as Moore's successor and Cheika suggested his time would come again after a strong season for the struggling Sydney-based Waratahs.
"Hoops, really improved out of sight this year with the 'Tahs," Cheika said.
"It's not been easy for him and he's excelled in the way he's handled himself."
With David Pocock on sabbatical and number eight Ben McCalman ruled out of the June internationals with a shoulder fracture, Cheika said his back row deliberations were not made any easier with the possibility of Melbourne Rebels flanker Sean McMahon heading overseas.
Despite the uncertainty over McMahon, Cheika said he saw the young number seven as a natural leader.
"No matter what decision he makes, I'll be looking at him taking that role if he's in the squad," added the coach.
"He's got strong reasons why he's thinking about it (playing overseas) and I respect those and understand totally and as always with Sean, he's a class act.
"I presented the counter view and he understood that too and he took it on board."
Australia play Fiji, Scotland and Italy in the June internationals.
(Reporting by Ian Ransom; Editing by Greg Stutchbury)
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