I don't know of any ship's manifest but the National Archives Records Administration has several microfilm rolls on Ship Island. They are 598, Roll 136, Volume 406; Confederate Prisoners at Ship Island, Mississippi and Volume 407 which has "Morning Reports for Ship Island" begining on December 3, 1864 some months after Confederate prisoners were first sent there.

National Archives Microfilm Publications
Microcopy No. 617, Returns from U.S. Military Posts 1800-1916, Roll 1167, Ship Island, Mississippi, January 1862-April 1870. This information is just general military matters keeping track of Union soldiers comings and goings, but occasionally mentions Orders and directives from higher headquarters.

I've been typing the Confederate prisoners' names [onto my computer] who were sent to Ship Island. It is a long process due to scarcity of 35mm mircofilm readers and copiers.

I've noticed the nineteenth century handwriting can make discerning an "I" and "J" difficult, as well as a "L" and "S" or "F" and "T".

I'm cross-checking with other Civil War records because some of the names are faded or the handwriting is difficult to read. Plus the fact it was photographed onto a 35mm strip.

The Ship Island prisoner list will tell you a soldiers unit, company, where captured and when; where sent from and where sent to. Occasionally there is a note for death or other information.

The prisoner list has already listed two names of soldiers who died on Ship Island but are not listed among the 153 Confederate soldiers already memorialized. These two soldiers are:

Thomas Gorman, The NATIONAL ARCHIVES MICROFILM PUBLICATONS, 598, Roll 136, Volume 406, Confederate Prisoners at Ship Island, Mississippi, Letter “G” page 106 line 1 lists Gorman on the officer page and page 108, line 55 lists him again with his date of death as October 3, 1864 [cause of death unknown] and the notation to “See Officers” under Unit and “See Officer List” at end of line. He was captured on August 5, 1864 on Mobile Bay.

Private D. W. Goode is listed on the NATIONAL ARCHIVES MICROFILM PUBLICATONS, 598, Roll 136, Volume 406, Confederate Prisoners at Ship Island, Mississippi, Letter “G” page 107, line 20; as having died on November 23, 1864. Cause of death is unknown.

I'm still working on the "G" prisoners and expect to find more Confederates who died on Ship Island as I type through the entire list.

It all supports a book length study I've been working on about Ship Island and the role it played during the Civil War.