Superman of course! He is the very symbol of heroism and goodness and his actions will forever change the universe for the better.
Batman and Superman will be equally responsible for the establishing of TJL. Bruce will probably, as many say, have a completely different role even if he is also a leader. Offically Supes is the leader and he could pull rank on batman, but would only do it under extreme circumstances. For instance, if Batman would give one order and Superman another, they would choose Superman even if Batman´s orders seem better. This isn´t likely to happen for Superman and Batman either agree or come to an agreement.
Superman will never order Batman, he will instruct him and Batman will do the same. In reality they stand equal between themselves. Outwards it´s Clark that is the leader. All formalities (such as press, lead a JL meeting, take responsibility for JL actions, be the one to welcome you to/fire you from the league) are in some way taken care of by Superman.
It´s hard to explain but I´m hoping for something like that.
What I said in the begining about Supes being symbolic, it has also to do with the fact that he will slowly grow into the role as #1 leader.
Even if Batman plays an equally big part as a leader/establisher in the beginning of the JL days.