www.alaskaferryvacations.com, and spoke with the very knowledgeable staff there. I told them what our dates were, what we were interested in doing and where we wanted to go. They told me they would call me back within a few days. Being a former travel agent, I just had to see if I was up to the challenge of figuring it out myself. And I didn't do too badly. But I am glad we left it up to Jo-Jo, our ferry specialist. She called me back when she said she would and we really liked her itinerary. So we booked with them by paying 50% down. Then after our final payment was paid, they sent us a coupon booklet for the ferries and all our excursions. We booked our own airfare into and out of Juneau plus our own hotels.
Our itinerary consisted of four different towns with an excursion in each town. In all 4 towns we had the town to ourselves after the cruise ships left. No waits at restaurants, no crowds to deal with and a chance to go to Sitka which isn't offered on all cruise itineraries.
The ferries themselves differ by what city they are going to. The largest one we traveled on had a movie theater, restaurant, lounge, tv watching lounge, coin operated laundry, and a heated solarium on the top deck. You are allowed to bring your own tent and pitch it on any of the outdoor decks for no extra fee. You could travel from town to town for just the ferry charge! which some people were doing. We met a man who had driven from Mexico to Washington and caught the ferry from Bellingham to get to Alaska.
I loved the ferry system and have nothing but good things to say about booking it, traveling on it or any of the amenities they had. I feel we were traveling the way the locals get around and not herded from town to town with hordes of cruise passengers. Sitting outside on a lounge chair watching the beautiful scenery go by and drinking hot chocolate - priceless!