Ouch, Chomsky man, a little googling would've done you well.

He means to refer to German Admiral Karl Donitz. Donitz had an extensive career in the German submarine force, culminating in his leadership position over the famed German U-Boats of World War Two (and eventually the head of the entire German Navy around '43). At it's head, he presided over an extensive campaign of unrestricted submarine warfare (much more important than how Chomsky casually waves off), and as such faced charges for it at the Nuremburg courts.

He was, in fact, found guilty on that very charge. US Admiral Nimitz did testify that the United States Navy had engaged in the same conduct of unrestricted warfare against the Japanese Empire in the Pacific. Due to this, Donitz never received an actual sentence to his guilty charge, but still spent ten years in prison after the war.

There was no Admiral Gernetz, but he's referring to the case of Admiral Doenitz. He was head of the Kriegsmarine's submarine force until 1943, when he was promoted to head of the navy. He would end up being Hitler's named successor, and surrendering to the Allies at Flensburg. As head of the U-boat force, he was responsible for that service's policy of unrestricted submarine warfare - submarines would torpedo ships without confirming that they were legitimate targets (belonging to a belligerent power, and carrying military cargo). They would also fail to render assistance to crews of sunken vessels. From the relevant section of the Nuremberg judgement:

Doenitz is charged with waging unrestricted submarine warfare contrary to the Naval Protocol of 1936 to which Germany acceded, and which reaffirmed the rules of submarine warfare laid down in the London Naval Agreement of 1930.

But Allied submarine forces carried out similar breaches of those protocols. British submarines were allowed to sink anything in certain regions near the German coast, while American submariners carried out unrestricted warfare against Japan. Statements to this effect were used by Doenitz in his defense, and he did use Admiral Nimitz as a witness:

In view of all the facts proved and in particular of an order of the British Admiralty announced on the 8th May, 1940, according to which all vessels should be sunk at sight in the Skagerrak, and the answers to interrogatories by Admiral Nimitz stating that unrestricted submarine warfare was carried on in the Pacific Ocean by the United States from the first day that nation entered the war.

This was sufficient for him to receive no punishment for this. He would however be imprisoned for use of concentration camp prisoners as slave labor and for enforcing the "Commando Order" (Any 'commando' captured by German forces was to be shot).

Source:

Judgment of the International Military Tribunal: Doenitz, H. D. de Vabres et al, The Avalon Project, Yale, available at http://avalon.law.yale.edu/imt/juddoeni.asp