Though since it would probably take at least a few weeks in-game to build the Tower (assuming metahumans build it), I'm thinking they can use an old Justice League base in the interim, similar to how the Team used Mount Justice in the Young Justice cartoon. The actual tower could be build on a secret island just off the coast from San Francisco, which is hidden from view using Martian cloaking technology. They can reach the island primarily through Zeta-Beam Transporters. More on that when Batman explains the Tower's details in-game.