I initially had the same concerns about citing Uboat.net until I did a search for other works that have cited the website. I came up with the following through Google Books, listing only those where I could see an actual citation:
Atkinson, Rick (2002). An Army at Dawn: The War in North Africa, 1942–1943 (1st ed.). New York: Henry Holt & Co. ISBN9780805062885. OCLC49383747.
Conley, Tom (2007). Cartographic Cinema. Minneapolis: University of Minnesota Press. ISBN9780816643578. OCLC73501932.
Lecane, Philip (2005). Torpedoed!: the R.M.S. Leinster Disaster. Penzance, Cornwall: Periscope. ISBN1904381308. OCLC74335239.
Treadwell, Theodore R. (2000). Splinter Fleet: The Wooden Subchasers of World War II. Annapolis, Maryland: Naval Institute Press. ISBN1557508178. OCLC43706924.
Whitlock, Flint; Smith, Ron (2007). The Depths of Courage: American Submariners at War with Japan, 1941-1945 (1st ed.). New York: Berkley Caliber. ISBN9780425217436. OCLC77503911.
Wise, James E.; Baron, Scott (2004). Soldiers Lost at Sea: A Chronicle of Troopship Disasters. Annapolis, Maryland: Naval Institute Press. ISBN1591149665. OCLC52182511.
Zuehlke, Mark (2008). Operation Husky: The Canadian Invasion of Sicily, July 10–August 7, 1943. Vancouver: Douglas & McIntyre. ISBN9781553653240. OCLC245556470.
There are probably more that are not visible via "Limited Preview" at Google Books. All appear to be major publishers, including one that's from an academic press. Some of the books have multiple editions; one has 23 different editions.
