Seat 2A, with your experience can you suggest towns to spend more days at after getting off the ferry? I have done a fair bit of net reading
First, since there's only one ferry in the entire month of May that can connect you from the southeastern communities (Juneau, Ketchikan, etc) up to Whittier, the odds are pretty good that you won't be on it. So the focus here is between Bellingham and Juneau.
If you're on an afternoon or evening departure out Bellingham, hopefully you'll have some time to visit Bellingham's Old Town, also known as Fairhaven. It's about a 3-4 minute walk from the terminal. Lots of old brick buildings, quaint stores and restaurants, etc. Also worth noting is that the Amtrak train station is practically across the street from the ferry terminal.
Along the way to Juneau, you might want to get off for a day or two in Ketchikan. I personally wouldn't want to stay any longer, not because Ketchikan's a bad place (rainy though...) but because you really don't need more than a day to see the place. I'd send a link to Ketchikan but because I haven't posted enough times at this site, I'm prohibited. Google it.
Juneau is the capitol of Alaska. It's definitely good for a day or two, but no more. Very pretty, mountainous location. Consider a helicopter flight up the Mendenhall Glacier, rent a kayak or go whale watching. There's plenty to do.
From Juneau, it's just a short ride (2-4 hours each way, depending upon a fast or slow ferry) up to the Lynn Canal to Skagway, a pretty little town that was the jumping off point for the Klondike Gold Rush. Consider a ride on the White Pass & Yukon Route Railroad. Again, this site won't allow me to post links, so Google some of this stuff for more info.
From Juneau, you'll have to fly 570 miles to get up to Anchorage and onto the main road system. A map of Alaska will give you a better idea. From there, anywhere you go from Homer to Valdez to Denali Park will be good.