Trains are very fuel efficient. CSX says trains can move a ton of freight approximately 492 miles on a single gallon of fuel. https://www.csx.com/index.cfm/about-us/the-csx-advantage/fue...
I suppose you'd have to factor in other issues in the "real" world, like managing inclines, curves, and starts/stops for traffic. Boats generally have fewer constraints on those fronts. Also, boats can increase their size in more than one dimension, which lets them increase size more geometrically and efficiently (trains can only get longer, and hits practical length limitations faster).