I have been pondering this for a few minutes, and I do not recall seeing any US Navy personnel ever mentioned for the Union's leased transports on the Missouri River in 1864. The Federals hired boats with crews and left them to operate as they saw fit with some guidelines about resisting capture and protecting their government cargoes. On some occasions land forces even with a cannon or two were placed aboard some boats to repel guerrilla boarders and prevent a repeat of the 28 March 1863 "Sam Gaty" capture that resulted in the murder of a number of black men aboard and two or three cavalry troopers. I would therefore conclude command of those transports (no naval war craft were on the Missouri in 1864 that I have read) fell to the U.S. Army quartermaster corps. I know the U.S. Army quartermaster corps was in command of the port of St. Louis, because they had to answer for all the boat sabotage at the levee done by the Confederate arson conspiracy bunch. You can search George and Deb Rule's civil war in st. louis website about the boatburners article, but I think that is what you will find.

Bruce Nichols