We have access to the Shinkansen from Hakodate down through Honshu. Prices for the bullet train are not cheap and, unfortunately, JR Rail Passes are not available to residents of Japan. However, the speed of the Shinkansen is certainly something you should experience at least once during your time here. To illustrate, a trip from Hiroshima to Kobe would only take 1.5 hours (compared to 8 hours by local trains) but it will set you back about ¥10,000. Tickets can be purchased at the ticket offices of stations that offer Shinkansen services.
Ferry ports in Tomakomai, Otaru and Hakodate offer services to various locations around Honshu from Aomori to Osaka. Hakodate to Aomori takes around 4 hours and costs about ¥2,000 for a one-way ticket, whereas Otaru to Kyoto would cost around ¥20,000 and take at least 24 hours. Reserve online tickets and pay at the ferry terminal.
Low cost carriers such as Vanilla Air, Peach and Jetstar offer one-way tickets from Sapporo to Tokyo for about ¥5,000 yen. Other airlines like ANA or JAL offer the same trip for ¥10,000 yen or more.
Flights are typically booked online with a credit card, though some airlines, such as Peach and JAL, allow you to pay at the convenience store.