As well as the various Ballard books, there is also this textbook on underwater archaeology which explains a lot of the terminology and covers most of the major (and minor) wrecksites up to the 1990s.

http://www.amazon.co.uk/exec/obidos/ASIN/0714127582/026-4150867-2858864

Had to mention it, as if you study the bibliography really closely, you'll find my name Though the boat in question wasn't underwater, well not all of the time anyway........

And there's also 'The sea remembers' if you can get hold of it

http://www.amazon.com/gp/product/1555840930/103-1206941-2571005?v=glance&n=283155

Here's two that I enjoyed reading a few years ago:
1. USS San Diego-The Last Armored Cruiser
By Gary Gentile ISBN 0-9621453-1-9
2. Shipwrecks of the Atlantic---Montauk to Cape May
By Bill Davis ISBN 0-923155-12-0

One that I realy like also is Ghost Fleet. It's about a crew of divers who dove the fleet that was sunk by the bomb tests at Bikini. They dove on a transport ship, the battleship USS Arkansas, the carrier Saratoga, and the Japanese battleship Nagato, among others.