Six's opening night was supposed to be the first night of the Broadway closure. They held the reviews and did not have a performance. I think the show technically didn't open. So the only musical with an eligible score would be The Lightning Thief. If the Tonys were held with only already-opened shows, I think The Inheritance might win this one.
With the timing of the closure right at the start of the spring deluge of openings, there are only five shows from this season that already opened that would still be playing on re-opening, at the most: Moulin Rouge, Tina, Jagged Little Pill, West Side Story, and Girl from the North Country. The Lightning Thief would be the only other eligible musical. No rulings yet on Girl from the North Country, but I don't think there would be an eligible Lead Actor under normal circumstances. I think Jay O Sanders and Austin Scott might get ruled as Leads to fill out the category, because I think only Aaron Tveit, Isaac Powell, and the Lightning Thief lead would otherwise qualify.
If those are the eligible musicals, I think the acting winners would be Isaac Powell, Adrienne Warren, Mare Winningham, and Danny Burstein. Not a bad list of honorees.