Two references that list Civil war shipwrecks are:

"Beneath the Waters, A Guide to Civil war Shipwrecks", by James E. Hemphill, C 1998, Burd Street Press, ISBN 1-57249-054-3

"Shipwrecks of the Civil War, The Encyclopedia of Union and Confederate Naval Losses", by Donald G. Shomette, C 1973, Donic Ltd. No ISBN on my copy.

Neither book is all inclusive, but do complement each other.

Bob