I don't know who would take over, but this would be a huge blow to the Kriegsmarine. Raeder was a proponent of a surface fleet and called for attacking through the Mediterranean while Doenitz revolutionized submarine warfare with his "wolfpack" tactics that nearly strangled Britain into submission. Submarines were the only thing Germany was able to outproduce everyone else in, including the United States.
Without either of these two, I believe the Kriegsmarine would essentially become a non-entity in the war. It might even be possible that with reduced numbers of German subs the Allies might be able to launch an earlier invasion of Europe since so much of their shipping wasn't sunk.