Although Juneau is the state capitol, most flights go in and out of Fairbanks or Anchorage, since they are larger and provide easy access to more of the state. Within the state, there are frequent commuter flights between cities plus charter helicopters and small planes providing transportation to the more remote locations. Several commercial cruise lines offer wonderful 4 to 7-day excursions departing from Seattle or Vancouver, Canada. They usually follow the coastline up to Prince William Sound and back with glacier viewing, whale watching and stopovers in Sitka and Skagway. A combined land-sea excursion often includes a visit to Denali and other interior attractions.
Cruises can be expensive, but they are a very comfortable way to see Alaska.
As a less expensive alternative, try the ferries of the Inland Marine Highway. Cabins cost extra, but you are welcome to spread your sleeping bag on one of the many chaise longues in the solarium or even to pitch your tent on the open deck. The trip takes about 3 days. The trains are very comfortable with large windows and domed observation cars for scenic viewing. Despite the harsh winters, this railroad runs all year round.