If Germany Had Somehow 'Perfected' The Atom Bomb Before The U.S. Actually Did During WWII....

Assuming they have by 1943, which is completely unrealistic, their best chances would be to use it against the Russians and bluff the western allies with threats of additional atomic bombings against the West if they don't sign a peace treaty or an armistice. 

That being said; Berlin will probably be the target of Little Boy.