John, I don't recall seeing a full roster for either vessel. This is due in part to the fact that the large majority of the men on board were soldiers, mostly drawn from volunteers from the Fifth Texas Cavalry, recently returned from the New Mexico Campaign, and Companies B and C of the First Texas Heavy Artillery. These men were probably on and off the boats again within 24 hours or so. Both boats were normally used as transports, and had much smaller regular crews in their normal operations.
A couple of other very small points. Neither Bayou City not Neptune No. 2 should carry the prefix "CSS," as they were never commissioned into the Confederate States Navy. They were officially part of the Texas Marine Department, a collection of boats and crews formed from former civilian steamboats and crews that ran in the area before the war, that was operationally under the control of the senior Confederate Army commander. There were two additional Texas Marine Department boats at the battle, Lucy Gwinn and John F. Carr, that served as tenders or support vessels to the larger "cottonclads." Neither of those were armed, or took part in the fighting that day.