The Leinster Lightning skipper hit 14 fours and 3 sixes as he top scored with 125 as his side racked up 337 for 9 before declaring with 14 overs remaining in the day.
Mooney shared a 5th wicket stand of 149 in 32.1 overs with Max Sorensen, who took the initiative away from the Northern Knights after an attritional morning session.
Sorensen cleared the boundary ropes four times and hit 8 fours in an entertaining 78 from just 103 balls, before being dismissed by left-arm spinner James Cameron-Dow (3-93).
Fellow CIYMS spinner Jacob Mulder (3-85) also picked up three wickets, but it was Leinster who dominated the afternoon and evening sessions after a poor start in the morning.
Shane Getkate (2-42) dismissed debutant Jack Tector (13) and Simi Singh (4), after tight impressive opening spells from Stephen Bunting and Robert McKinley who bowled 15 maidens between them.
Instonians left-armer Bunting (1-49) bowled Andrew Poynter for 9, and when Mulder ended Fintan McAllister's obdurate vigil (16 from 88 balls), the Knights were very much in the ascendancy with Lightning 56 for 4 just before lunch.
Mooney and Sorensen's counter-attack changed the momentum of the contest, but the Knights battled bravely in the final hour of the day to give them real hope of securing enough points to claim the Championship. If the game is a draw, they need to score 250 in their innings to pip the Warriors to the title - having earned four bonus bowling points.
An opening stand off 41 between Chris Dougherty (20) and James McCollum gave them a solid platform to do just that, before Dougherty was dismissed with just nine balls left in the day. The left-hander cut Tyrone Kane straight to Jack Tector at point to give Lightning a late boost.
With nothing less than a win enough for Leinster Lightning to secure the title and complete the clean sweep of Hanley Energy Inter-Provincial titles, it promises to be a fascinating second day at Rathmines - the action resumes at 10:30am.
HANLEY ENERGY INTER-PROVINCIAL CHAMPIONSHIP
At Rathmines, Day 1 close of play
LEINSTER LIGHTNING 337/9 dec (87.4 overs. J Mooney 125, M Sorensen 78, T Kane 29, E Richardson 25*, J Mulder 3-85, J Cameron-Dow 3-93, S Getkate 2-42)
NORTHERN KNIGHTS 49/1 (14 overs, C Dougherty 20, T Kane 1-8)
