If it were between the FFXII chocobos and moogles, then it would get a little harder to decide. Moogles were a main race, equal to humans, bangaa, viera, and seeqs. And The Craftsmoogles Guild, while fairly unorganized, was pretty damn cool, not to mention helpful in getting to fight the Hell Wyrm* and providing good filler in between the main pieces of the story. Also, there were hostile chocobos in XII, which makes it harder to vie for them. But chocobos and moogles from any other FF are a clear decision in favor of the chocobos, which means overall the chocobos still win.
*Not putting spoiler tags on a game that's over five years old.