You kind of need to be more specific about what you mean by sovereign. Federal pre-emption exists[0]. There are lots of ways in which the federal government can enforce their will (constitutionally!) on states.
But it's super complicated, and in this particular case does the state have some special right to name the body of water it's adjacent to that pre-empts the federal government? I dont know. Probably not, but I think the argument would need to be more explicit about what that right is rather than just claiming states are sovereign.