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Getting to Omagari
The nearest airport to Omagari is Akita. Tokyo has 2 airports, Narita and Haneda, and if you land at Narita you will need to change to Haneda to get a flight to Akita. There are several flights a day so connecting from an international flight is usually convenient.
There are direct flights to Akita from two other airports in Japan, Sapporo and Nagoya.
By Shinkansen Bullet Train
The other travel option from Tokyo is the famous Shinkansen bullet trains which have direct service to both Omagari and Akita. It is a nice way to travel but it does require a couple of connections by train and subway to get from the terminal to the shinkansen station and if you are traveling with a lot of luggage you may find it less tiring to travel by plane.
From Haneda airport, take Tokyo mono-rail to Hamamatsu-cho station (16 minutes), change the train to take JR-East to Tokyo station (6 minutes) and change the train again to take Shinkansen to Akita or Omagari.
Akita Shinkansen from Tokyo to Akita takes 4 hours and 3:30 to Omagari and departs every hour from 6:00 to 20:16.
The Japanese train system is extremely punctual and sometimes using trains might be faster than flying when you take into account extra waiting time, baggage claim time, transportation from and to airport, etc.).
Also JR has Japan rail pass system for foreigners and trains might be less cost than flying.