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.
Agreed! It's a complicated argument that would have required detailed discussion. But Google found it more politically convenient to bow to Trump and make it a fait accompli. Thus Trump makes an incremental step further towards his dreams of dictatorship. What will Google do when Trump tells them to rename a city, I wonder?