If you take AirAsia. It will arrived Midnight. No that simple anymore. 
Normal daylight.  2Way
Yeah, I'll be arriving midnight. I was thinking of staying at the airport hotel before we start moving the next day. I'm not sure by what you meant with "Normal daylight. 2way" but I assume that youre recommending we travel during the day?

1st - Just take keikyu Airport Line to Shinagawa Station then change to Yamanote Line to Tokyo Station then Nagano Shinkansen to Nagano Station.
2nd - Take Haneda Monorail to Hamamatsucho Station then change to Yamanote Line to Tokyo Station Then nagano Shinkansen to Nagano Station.
Thanks for the route recommendation. The second option is the one I consistently come across so I think I'll go with that.

Yes, With no Seat Reservation. It will be First Come first serve.  If Holiday season. You need standing at Non Reservation section all the way to Destination. Like our KTM commuter train.
The trip is gonna be about 1 hour and a half from Haneda to Nagano. I think I'll opt for the seated option although I wont be traveling during their Holiday season.

If you're travelling to and from ski areas, there will be space inside each Shinkansen bullet train carriage for large ski/snowboard bags - please let the conductors know when you board that you'd like to stow them. In addition to this there is the standard area for luggage inside each shinkansen carriage: overhead storage and behind the last seats in the carriage, though these can get crowded.
I have never been inside the bullet train before but I'll assume that ski bags that are 160cm in length wont fit the overhead compartments. How do I inform the conductor beforehand? Will he help me unstow it when I disembark?

Station concourses can get busy, especially during rush hour, so you should try and keep your gear as tightly packed and as easy to move as possible. Ski/snowboard bags with wheels are a good purchase.

If you really have a lot of things, consider using the Takyuubin delivery service, which is incredibly efficient at getting your items to the right place. You should be able to send your skis and other equipment direct to your hotel from the airport with a next day service, and is highly recommended. You can use the same service to send your equipment back to the airport.

Finally, if you need to do some more travelling once you are away from the slopes, you can store luggage at the left luggage counter available in most stations. The left luggage counter in Tokyo station, for example, can hold onto items for up to 15 days.
Thanks for the info, I can see how this is going to be useful.