@josie a couple of thoughts.
We took a trip where we rented a van and camped out for two weeks in Alaska and followed it up with a cruise back down the coast to Seattle. Two weeks of fending for yourself topped off with a week of pampering and overeating. Icing on a cake.
As someone else mentioned (@Tropical_Willie) you can get a combo land/sea tour through the cruise lines. These are tightly scheduled, you will not be able to customize what you do, where you go or how long you stay. You go where they say you will and when they say you will.
If you choose to do a southbound trip be sure to end up in the US (Seattle) and not in Vancouver. Getting over the border back into the US has been a time consuming royal pain in the ass both times we have done it. If you do choose a cruise that ends up in Canada, pay the extra to fly back from there. A couple of years ago it cost a little over an additional $100.00 per person to fly from Vancouver over Seattle but in retrospect would have been well worth it.
Northbound trips give you the choice of either leaving from Seattle or Vancouver. It is cheaper to fly to Seattle and you can rent a car or take the train to Vancouver. Crossing the border this way means being prepared to wave at the border guards as you whip across. Or you can just fly into Vancouver for a little extra.
Round trip cruises give you the advantage of returning to the same port and make booking air passage a little simpler. The downside is that you actually spend less time in Alaska, Seattle itineraries require a stop in Canada to meet U.S. regulations, round trip sailings often only visit three ports in Alaska and offer one day of scenic cruising, whereas one-way sailings might visit four Alaska ports in a week and/or offer two days of scenic cruising . The other thing is it limits you if you want to spend time doing some land exploring in Alaska.
The cruises we took left out of Seward (this is the small town south of Anchorage). We took the early morning train from Anchorage to Seward. A very rewarding experience. My wife enjoyed the comraderie on the train (many or most of the passengers are also going on the cruise) and I spent almost the entire time in the area between cars taking photos of the countryside starting with the sunrise and the mists rising off the many bodies of water, the mountains shedding their shroud of clouds and the small towns and villages you pass through. I was half frozen by the time we got to Seward but the resulting photographs were worth it.
Get an outside cabin so you can sit on your balcony on your journey and choose the side based on whether you are going northward (starboard) or southward (port). You want to be on the side with a landward view. Although to be fair you will be in the Inside Passage so there will be land on both sides most of the time so don’t stress if you cannot get the side you want. Also, my wife does not feel the need for a balcony; she is content with an outside view.
If you get the opportunity go to Homer. It is a quaint little drinking village with a fishing problem. I have a photo of a bumper sticker on a rusty truck (in Alaska this is redundant) that says “Homer – We’re here because we are not all here”. You can probably only do this if you spend time ashore as well as cruise.
While the big cruise lines do take you to view glaciers it is a much more rewarding experience to take a smaller vessel if you can work it into the schedule. We used a company called Stan Stevens Glacier and Wildlife Cruises out of Valdez to view the Colombia Glacier. They were very attentive and informative. I would probably have enjoyed a smaller vessel but the one they had was only about half full (or half empty, I don’t recall which) and as it was a six hour trip it was nice to have the wandering room. There are many other companies out there. The main thing is to get on a smaller vessel and more up close and personal with the glacier.
Some of the ports can be somewhat limited in what you can do just wandering around and your time will be limited in many cases so think seriously about getting on an excursion. Whale watching, wildlife tours, plane rides, train rides, historic tours, halibut fishing trips etc.
Shore excursions will be slightly more expensive than if you set them up yourself through local land based companies (the same ones the ship uses) BUT if you book through the ship and the excursion is late getting back they will wait. The same courtesy is not given to independent tours; if you are late finding a way back onto the ship is your problem and usually entails getting to the next port of call somehow. The ship will emphasize this in an attempt to get you to use their services. That being said, most independent tours are well aware that their livelihood depends on positive feedback and will make sure you are back in plenty of time to make your departure.
Skagway has a pretty good brewery toward the end of the main street. Their Blue Top Porter is passable and if they have any left try their Spruce Tip Ale but it is seasonal and supplies are limited.
If you don’t do the open seating as @JLeslie suggests, and I prefer not to, then get the late seating. This gives you time to enjoy your stops, get back to the ship, maybe grab a snack at 5 pm and still be hungry at the 8:30 dinner slot. We prefer to have the more formal setup because, for us, part of the enjoyment is coming together with the same people each evening and discussing our days events and getting to come to know them better over the course of the cruise. We prefer this to sitting with strangers at dinner each day; you can do that at breakfast and lunch.
I believe that, while everyone has their favorites, most of your bigger cruise lines are comparable in price, comforts, foods, safety, etc. They even have very similar itineraries. So the thing to do is find the one with the best price that goes to the places you want to see.
It is worth your time and you will both enjoy it. Let us know how it goes.