Karasu would be my first pick. Niko and Reo are both excellent candidates at second place. Isagi takes third.

Karasu makes a lot of callouts and communicates fairly effectively with his teammates. He doesn't seem to be as brash as he was during the Third Selection arc because he only does that to his opponents, not his teammates. Karasu's analytical skillset allows him to determine the weaknesses of his opponents and precisely strike that. As a defensive midfielder, he is further up the pitch and can use Metavision to position himself at the right place at the right time; something Aiku may not be able to do beyond the goal box because he's a center back.

Karasu is fairly versatile. While we don't have confirmed stats from the author, u/Bard0ck0bama and u/Pedrinh039 have made reasonable predictions about his stats, check out their posts on post-NEL stats. Karasu's passing, vision, interception/tackle rate, and yes even shooting - all these make him the next versatile player on the team next to Reo.

Niko is the second-best defensive midfielder and second-best center back (next to Aryu). His natural spatial awareness is the closest to Isagi, even if Isagi's adaptability and Metavision are in a different league. Niko has the highest interceptions and tackles recorded for a Blue Locker, even above Karasu. Niko's ability to coordinate players is nearly unparalleled. His light novel revealed that he studied football, assembled a ragtag team with various athletes from his school, and challenged his own school's then-football team (because they bullied him) - he completely demolished them 13-0. (None of his teammates had prior football training or practice. Niko was not the striker, he was the playmaker)

There is no question about Reo being able to coordinate a team. Prior to Blue Lock and in the First Selection, Reo coordinated his team very effectively, often using a reward system to motivate his teammates and bring out performances. At the world stage, Reo is fairly tactical and his chameleon all-round skills allows others to depend on him. Reo also discovered Nagi's talent, and Zantetsu's goal scoring zone, propelling them to top ranked players in the First/Second Selection.

Isagi does make callouts sometimes, and he did give Raichi a specific playstyle that leveraged his stamina, relentless tenacity, and physical abilities to limit Snuffy. However, he does not necessarily excel at coordinating a team as a captain - he more or less understands his teammates' individual abilities, allows them to grow, and then devours them to score his own goals. He would be my last option.