I took a road trip there May and June. We drove to Bellingham, took the marine highway to Whittier, drove all over the place ending in Skagway, then took the marine highway back to Bellingham. The Amtrak station is across the road from the ferry depot in Bellingham. It is not really pedestrian friendly, but not unfriendly either, you won't have any trouble walking it with luggage but some people would.
We saw cruise ship people in some ports and I emphatically suggest avoiding that.
People fares on the marine highway ferries are downright cheap, rooms are comfortable and reasonably priced. Taking my car was the most expensive part but I'll probably keep taking it on future trips just because it is easy.
We took food on the ferry but ate one hot meal in the dining room each day. The food was good and priced under Amtrak. The special sells out early. As in Alaska, chicken is expensive but fresh fish is cheap. Tips are banned! With signs that any tips found would be considered a gift to the state general fund.
On the ferry, I'd suggest getting off in several ports for a day or so. Also, everybody talks about the Inland Passage and it is definitely special, but the trip across the Gulf of Alaska was truly awesome. There are several inland passage routes and if you work out the stops and ships right, you can take different ones northbound and southbound. There are plenty of transit options on the islands. If it were me and I didn't have a wheelchair, I'd figure things out in each port at the last minute, but you kind of like things just so, so I'd recommend at least getting phone numbers and schedules in advance.
The
Alaska Railroad runs trains hubbed in Anchorage. So the timing is great if you are in Anchorage but want to go fishing for the day in (for example) Whittier, it is rotten if you are landing in Whittier in the morning and don't want to spend the day in Whittier (although there are some great hikes there)! However, the people on the ferries are friendly and you are very likely to meet someone who has a car in Whittier (or anywhere else) and will be happy to give you a lift.
Hang out in public areas and meet people, including the backpackers with tents on the deck, they know how to get around without scheduled service and will happily add you to their carpool. You'll also find families returning from shopping or medical appointments in Juneau who will be happy to fit you in. I always do that kind of travel with a pocket full of small items that say "California" on them.
I did the trip this year with my brother and S-I-L because he had some use-or-lose vacation and it was getting hot where I live. It was fun sending photos of thermometers up there of 72, to people back home baking at 105. I made all reservations about 2 weeks before we left. The ferry stretch from Juneau to Whittier didn't have car space available so I got a ticket for me and my car to Haines (brother and wife to Whittier) and got in the standby lane, with success.
I've done two other Alaska trips. One was another road trip, ferry to Skagway then drive back through Canada. One was at Thanksgiving, flew to Anchorage and rented a car for a couple of weeks, then ferry to Juneau and flew home. After your summer trip, you might change your mind, get the right kind of clothes, and go see the Northern lights. This is another trip you take on short notice so you time it right.
What everybody says about limited winter schedules is all well and good but not enough to abort the trip if that is the only time you can take it. I'm saying this even knowing you like everything planned right. The locals are incredible. Maybe they have a tradition of stories about the stupid tourists. You will be able to find your way around even if it means hitching a ride with some kid whose mother you met in a cafe and she knows the kid is driving to town tomorrow, and btw, would you like to come to dinner tonight at her house, she has always wanted to go to Florida. I am not kidding or exaggerating here.
And Penny, I have 5000 photos from this trip still unsorted, planning on working on them on the train to the Gathering, be happy to bore you if you want to take a look!