Well it isn't going to be a Borg or Tholian vessel, that much is for sure. It would be stupid for anyone to own a Borg vessel, and highly impractical for anyone to own a Tholian vessel (the temperatures in them would be too hot, plus their internals wouldn't be suited to humanoids.
I was thinking the Andorian Warship, but alike the Vulcan Science Ship, I think they'll save the Andorian vessel for the C-Store (it makes sense). I can't see them giving out Breen vessels either, just doesn't seem reasonable, nor realistic; not that the Galor or D'Kora seemed realistic, but hell. Could be a Terran ship, though I can't imagine that working that well for the KDF side. It would practically be giving KDF players a FED ship.
Maybe they'll give us an Xindi Aquatic Battleship and our Bridge Officers are all given diving gear? ...or not. One thing that it could be, that nobody has yet suggested; a Son'a Battleship. The Son'a (some of them at least) were seen reconciling with the Baku at the end of Insurrection. It's possible they may have lent their ships out to the Federation (aiding the Baku) or the Klingon Empire (those who still want to destroy the Baku). That's my best (and probably worst) guess.
It wouldn't surprise me too much if there isn't another lock box planned yet. Just because one is ending, doesn't mean another one is just around the corner.
A Breen ship has been long rumoured but given that the Breen arc has been out for a long time, I could see it being in a random races doff pack, Breen, Deferi, anything else they might want to throw in.
Having trouble with ground STFs? Looking for help?
It will be stocked to capacity with Tranya.
And have an annoying little alien who condemns you for your war crimes everytime you visit your bridge, but then just gets you drunk on Tranya.
After 3 seasons he will grow up to look like RORSHACH from the Watchmen movies, and leave you to pursue Justice.