I used Deep Powder Tours, I just do a full package.
Flights + Bus tranfers and Accomidation.
They have heaps off accomidation too choose from budget backpackers through to 5 star, so its up to you to choose what you need and what your budget is.
Its very well run, heaps off info is supplied, they meet you when you land, put you on a bus. When you arrieve in the town someone meets you and shows you around the town and drops you off at your accomidation. If you have any issues they are your point off contact for the whole trip.
This was our first Japan trip and had zero needs or issues.
Then its the same deal when leaving, they pick you up and organize everything.
Me and my mate found it quite a relaxing way to travel.