Got JR weekend packages from Tokyo to both places from a local travel agent in Tokyo (Shinjuku). Can't remember how much they were, but think that the packages were about the same to both places, just a bit more to Naeba, but the hotel in Naeba was much nicer.
The JR packages include shinkansen, hotel, half board and liftpasses. Don't think that there is any information available on them in English though.
Check out
www.snowjapan.com: you should be able to find info on different options and packages through the site (or at least trough the discussion board they have there).
