Until somebody finds an actual list of fares, we can guess around 2 cents per mile; it might have been an even $20 one way on the direct routes (New York Central and Pennsylvania), and it might have been a bit less on the slower routes (Erie, DL&W/NKP). The faster trains probably cost extra; in the 1920s the regular fare entitled you to a 28-hour trip, and a faster train would cost you $1.20 per hour saved-- so the 20th Century or Broadway cost $9.60 extra.
None of this includes the charge for a bed.