We flew into Vancouver with Air Canada and were very impressed with them. We stayed at the Pan Pacific Vancouver, which is literally just above the cruise terminal. It couldn't have been more convenient.
We did the adults only Yukon Suspension Bridge, City and White Pass Railway tour in Skagway and that was superb. I can thoroughly recommend taking the railway in Skagway and you can easily wander around the town from the ship on your own.
In Juneau, we did the whale watching and Mendenhall Glacier, and again both were well worth doing.
In Ketchikan, we did flight seeing, which I'm guessing from your question won't be of interest to you but again, you can easily wander around the town on your own from where the ship docks.
Have a wonderful honeymoon cruise!
In front of the beautiful Chateau Frontenac in Quebec City as part of our Bagman Days trip, which starts with north eastern America and eastern Canada. The trip report continues for our Baltic cruise.
I also did the White Pass Railway excursion in Skagway, and loved it. The round-trip ride still leaves time to explore the town a bit before or after. In Juneau I was booked for the Mt Roberts Tram and Mendenhall Glacier, but the day was incredibly foggy and rainy, so I opted to just stay on-board. I did the Misty Fjords boat ride in Ketchikan and loved it, but it took up all the time we were in port and I would have loved a bit more time to explore the town a bit. Your itinerary is a bit different (I sailed from Seattle), so maybe you'll have a longer port-day in Ketchikan and can do both.
Have a great cruise! I'd love to do this one again some day.
"Best airline" will depend on your airport. There may be direct flights, or you may have to take one or more connecting flights. When you have a lot of choices, then there's also best for price or best for service. With fewer airlines to choose from...
For me, flying from Detroit Metro, both Delta and Air Canada provide convenient flights, with Delta usually lower-priced (and I'm happy with their service). Your situation may be different.
As to hotels that are "close by" - the terminal is in downtown Vancouver, so you have dozens of hotels to choose from, from mid-priced to super-deluxe, many within walking distance (though dragging your luggage more than a few blocks may not be worth your bother). There's even a top-flight hotel right in the cruise terminal - you just take an elevator down to the cruise terminal. Even if you stayed at an airport-area hotel, you'll be a 25-minute drive from the port. We cover some of the choices in our DCL guidebook, but we could only scratch the surface.
As to shore excursions that are reasonably-priced and don't entail flying... the vast majority of excursions fit into that category. There are some high-priced excursions that include helicopter flights to glaciers, or float plane flights through Misty Fjords, but again, there aren't many of those.
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We're going as a family in July (hopefully, still waiting for word that I will be granted the time off).
My oldest and youngest DDs went last July with oldest DD's husband and mother-in-law. They sailed from Seattle, so can't help you there.
Something that they said they really enjoyed and are hoping to do again is the sled dog place tour. They got to see sled dogs at work, ride a sled, and hold puppies (I think this may have been the best thing for them, as they were both missing their dogs). I have no clue what port this was in.
I will be getting to the excursions in the next day or so. We did the whae watching, glacier and lodge lunch in Juneau, the rainforest expedition in Ketchikan and the railroad in Skagaway with time on our own for exploring.