A lot of RRs owned them........including roads you might not think of, like Milwaukee Road and Santa Fe. It was definitely more common on the east coast though.
Southern RR had many tugs and boats, mainly in Virgina. I would think that just about any RR that served a port, either had their own "fleet" or had access to one.
Even the small Terminal Railways of Mobile, had 2 tugs and a couple of car barges. They were used to transport cars to several plants across the Mobile River from the main port. There wasn't room for a bridge and they couldn't afford to put one there, due to the amount of shipping, (Real ships).
PRR, B&O, CNJ, LV, NYC, Erie, DL&W in the Port of New York/ New Jersey
Reading - Delaware River, NJ, DEL and PA
B&O Port of Baltimore
PRR, C&O (Sou?, N&W?) Norfolk, Hampton Roads.