I've cruised Alaska 3 times now, on RCL (7-day from Seattle), CCL (10-day from San Francisco), and most recently Princess (14-day from Vancouver). The best experience we had was probably the Princess cruise - better food, we got to sail through Glacier Bay National Park, and it was a nice long trip (7-day back to back's from Vancouver - Whittier and Whittier - Vancouver). Princess also offers land tours, e.g. Vanouver - Whittier 7-day cruise + 3 days in their lodges to visit Denali. I haven't done that, but friends said it was nice. We didn't want the 9-hr train ride since we took a 15-month old with us that trip, and preferred to just stay on the ship and round-trip it (we saw Juneau, Skagway, Ketchikan, and GBNP each twice. We saw College Fjord on the way up and Hubbard Glacier on the way back.

As far as timing, if you go later in the season the mosquitos (AK state bird) will be out in force. We went June 8-22 this year and only really saw them in Whittier on 6/15; the rest of the stops we didn't see many, but we didn't do a lot of hiking in the woods either at any of the stops.

Side of the ship doesn't matter much; you'll be going up the inside passage so you'll be able to sit on the balcony and watch the scenery go by from either side. I didn't notice much difference in wildlife from either side, on any of our trips. I'd definitely get a balcony if you can swing it; there's a lot more scenery in Alaska than say the Caribbean (which is mostly just looking at open water unless you're in port). As you cruise the passage and get closer to the glaciers, you'll see seals on the ice flows, sometimes see whales, etc.

ALL the pools on the Sapphire Princess were heated this year, including the outdoor ones. They'd be steaming in the mornings on the back deck. There was also an "indoor" pool there which was nice - you don't freeze in the wind when getting out to dry off. The pools on the RCL ship we sailed in 2017 were not heated, so we only used the hot tub. I don't recall on the CCL Miracle but don't believe Carnival heats any of their pools.

If you need excursion ideas or providers, shoot me a PM with your email address and I can send you all my stuff from our 3 cruises - who we booked with, what we did, costs, etc. You can also get a lot of ideas over at the cruisecritic forums. And before you book anything, once you figure out some dates and ships, it's worth submitting a request on cruisecompete - it's a reverse auction for travel agents to bid on sailings. We've gotten some incredible deals that way (e.g. 14-day cruise out of Rome for 2 people in a balcony for $3400 TOTAL (not each)).... vs. $6500 direct from the line or other travel agents. After I booked, they threw in 2 free dinners at the steakhouse on board, in addition to some OBC, as a thank you.