I've got the same dilemma. I see that you can book the basic 2.75 hour train ride directly thru the railroad and they have a few more time options, plus it's cheaper. If booking w/HAL, we can only choose 8am (too early for me) or 12pm, which then conflicts with other tours we want to do. Has anybody booked directly thru the railroad? They do have this on their website:
For passengers arriving via cruise ship, this tour is available from your ship’s Shore Excursion Department. By booking through the cruise line, you will be able to take advantage of the dockside service and board the train on the pier alongside your ship. Contact your cruise line’s Shore Excursion Department for more details.
Is it really easier to get to the station if you book thru HAL?