Flash (super fast thinking), Superman, Cyborg, Wonder Woman, Batman, Martian Manhunter, Green Lantern (by proxy of the ring), Shazam (by proxy of the S in Shazam), Steel, Atom, the list goes on and on.
There are different levels and versions of genius. Superman and Flash had the gift of super-fast thinking, but they lacked the detective's intuition of a Batman.
You had the Einsteins of their day, Luthor (possibly another villain or two), the modern day Mr. Terrific, etc.
You had the super-technicians, Blue Beetle and the other heroes that "invent" their super weaponry.
And you had those with pure wisdom. Captain Marvel by way of Solomon, and Dick Grayson by way of his upbringing by Batman and Superman.
There was a Justice League arc in the 2000's that had the JLA presumed dead, and Batman's contingency plan kicked in, informing select heroes that they were now members of the new JLA. The pre-selected leader of that team was Dick Grayson, which to me was the obvious choice.