I think when you start you would use the river as it would require less work to get things going. You also can move greater volumes using less fuel and man power. Dredging and port facilities will be a concern, but less so than inspecting, repairing, and securing over 1000 miles of tracks.
Long term just as in real life the railroads will win when you consider the difficulty in offloading and moving materials away from the river. That will eventually eat up your efficiency gains once you have to deliver materials to multiple inland locations.
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