I spent some time doing killer whale research up in Whittier Alaska, it's on the Prince William sound.  To get there, you traverse a 2.5 mile tunnel that alternates between cars and trains.  When we did it, about 15 years ago, we drove the car onto a flatbed railcar and rode the train in, not sure how they do it now.  Prince William Sound is beautiful, I didn't do this 
tour, but it looks pretty interesting.