To answer the original poster, my top five would be
1. A History of the Confederate Navy (Raimondo Luraghi) – so good it inspired me to write two ACW naval games.
2. Thunder along the Mississippi (Jack D. Coombe) – a great one volume read on the Mississippi campaigns.
3. From Cape Charles to Cape Fear (Robert Browning).
4. Capital Navy (John Coski) – wonderful study of the naval war on the James River. Fabulous line drawings of the ships too! Inspired me to write my third ACW naval game. (The aptly named Anaconda: Capital Navies)
5. Lifeline of the Confederacy (Stephen A. Wise) – excellent study on blockade running during the war. There is a game in there somewhere, but I have not had the time to suss it out yet.
Also rans that could not make the top 10
Infernal Machines (Milton F. Perry) – everything you want to know about torpedoes and submaries.
Navy Gray (Maxine Turner) – a fascinating account of Confederate shipbuilding efforts on the Chattahoochee and Apalachicola rivers. Turner synthesizes ship building and the cultural background of the South and constructs an engaging narrative.
Arming the Fleet (Spencer Tucker) an encyclopedic entry into the obscure topic of naval ordnance leading up to and including the ACW.
An obscure monograph on the Confederate blockade of Washington D.C. Small battles with small guns that had a big influence.
Union Jack's and Life in Mr. Lincoln's navy provide two competing images of naval life. Ringle's seems more upbeat while Union Jack's presents a Navy that feels more human.
No one mentioned Silverstone's compilation of ship data. Without that we'd be hard pressed to generate data for some of the games.