Midfielder Cowie (right) picked up a slight knock during Thursday night's 2-0 defeat to the Hammers at the Cardiff City Stadium, while full-back McNaughton missed out due to a calf strain sustained in the 2-1 final-day win at Crystal Palace.
"Don took a little knock the other night, but he should be fine," Mackay told his club's official website.
"We're also hoping to have Kevin in the squad. He did well with the physios on Saturday.
"He will travel with us and was desperate to be involved on Thursday, though we knew it could have really hampered him longer term if he'd have gone out there to have a go."
The Bluebirds are battling to avoid a third consecutive play-off disappointment having lost the 2010 final to Blackpool before departing at this stage against Reading last term.
West Ham once again have a fully-fit squad available.
The Hammers picked up no new injuries when they ran out 2-0 winners in the first leg on Thursday.
Two-goal hero Jack Collison is set to keep his place despite still recovering from cartilage problems which mean the Wales midfielder sometimes sits out training.
Striker Carlton Cole, who has also struggled with a knee problem at times this season, should continue up front alongside Ricardo Vaz Te.
George McCartney has come on as a substitute in the last two games after recovering from concussion and is pushing to reclaim his spot at left-back, which would allow Matt Taylor to move to his preferred midfield position.