Tokyo Base was a Federation facility.
In the mid-24th century, Kyle Riker worked out the Fuurinkazan battle strategies at this base. Afterwards, he was asked to come to Starbase Montgomery, where he would work as a tactical advisor to Starfleet, a position he accepted. (TNG: "The Icarus Factor")
This facility was only mentioned in dialogue.
According to the Star Trek Encyclopedia, 3rd ed., p. 513, Tokyo Base was a Starfleet facility.