I live in Juneau, AK. Even though Juneau is not an island, it is still land locked and there are no roads out. You can ONLY get out by the ferry system, private boat, commercial jet/plane, or swim really well for 90 miles.
I took the ferry 12 years ago to move to Alaska. Definitely do some research about where you're going and the ferry route and ports. BTW, the system is owned and operated by the State of Alaska, NOT the US government.
They check your passport and ticket upon entry, and ask that you declare specific things especially if you are bringing a car, but there is no traditional security or TSA/airport type process.