I've just finished reading Timothy Mulligan's Lone Wolf: The Life and Death of U-Boat Ace Werner Henke (Praeger, 1993). I was really impressed by the way that Mulligan collated U-Boat war diaries, Kriegsmarine high command records, and Allied naval records to create a rich, contextualized account of Henke's career.
I have two more U-Boat books on the way, U-Boat commander Peter Cremer's memoir and a biography of Wolfgang Luth by Jordan Vause, published by the Naval Institute Press in 2001.
My question, though, is: what are the best academic/archive-based books about U-Boats during WW2? I'm looking for work that shares the strengths of Dr. Mulligan's rather than memoirs or trade press books.
Off of the top of my head, the two books I usually recommend are,
Wolf Pack: The Story of the U-Boat in World War II by Gordon Wiliamson. It's a book published by Osprey if you're familiar with that publisher. It gives a pretty good overview of the U-Boat program and it's development (including the interwar years), the training that went along with it, etc. I will say the illustrations that go along with the book are incredibly well done (though it's not the sole reason why I'd recommend the book).
Hitler's U-Boat War: The Hunters, 1939-1942 by Clay Blair is a pretty good book as well. Gives a great overview of the opening stages of the U-Boat campaign against the Allies and ends towards the end of Operation Drumbeat. There is a second volume in the series but I have yet to read it, though I've heard while it's not as good as the first volume, it's still well researched.