Dem Kommando der Schiffe und Boote der Luftwaffe unterstanden von 1940 bis 1945 alle seegehenden Fahrzeuge der Luftwaffe.
roughly translated
All vehicles able for duty at high sea of the air force were subordinate to the command of the ships and boats of the air force from 1940 to 1945.

You can find a list of all ships and boats of the air force here: http://de.wikipedia.org/wiki/Liste_von_Schiffen_und_Booten_der_Luftwaffe_von_1935_bis_1945

Martin