You can take the Silver Line for free from Logan Airport. Depending on the amount of stuff you have, you could walk from Silver Line Way about 15 minutes (hard with lots of luggage) or take it all the way to South Station and switch to the SL2 to go out to Dry Dock at the Design Center. That's about a five minute walk.
There are also water taxis - I haven't taken them, but it's another option.
It's right near Wall Street, so you can see the Charging Bull statue.
One of my absolute favorite things to do in NYC as a tourist is to ride the Staten Island Ferry. The website says it is ADA compliant, and there is a number you can call for additional information. It's the best free ride in NYC.
Portland is definitely walkable without an excursion, so I recommend not Portland. There is so much good food, a lovely promenade along the water, and option for an inexpensive boat ride on the harbor via the mail boat runs.
I found Lyft to be convenient and reasonably priced as well. I took a taxi from the airport to my hotel - it was certainly convenient (the was a long line of cabs), but it was both not very nice and expensive. But given my suitcase got absolutely drenched between getting off the plane and getting to the luggage carousel, it was worth it for me to just go out the door and into a cab.
I really like the walk along the Eastern Promenade as well - but definitely do the Mail Run (or any of the other options they happen to be running, like the Diamond run). If you are short on time, you can just do Peaks Island and back (I think you can just stay on and ride the ferry back).
I live in Boston (and used to live walking distance to the cruiseport). You might have better luck with Lyft or Uber than with a cab in Boston, but all are available. Olde Towne Trolley is the most prevalent hop on hop off bus, and they have a stop near the cruiseport (although you may want to double check for your sailing date). Harpoon Brewery is very close to the port and a fun visit, as well.
On smaller ships like Adventure, there will usually either be one at 7ish or two shows, one at 7ish and one at 9:15ish. On every cruise I've been on, I've gone to the show at 7ish and then straight to dinner. It works out well. You also should be able to get out of dinner for the second show, but I don't think I've ever done that.
It is a longish walk, but you can do most of it along the Harbor. It's probably 45 minutes plus. You can take the Silver Line to South Station and then the Red Line to Park Street. Or a Lyft/Uber. If you go that route, I'd recommend walking to the Design Center (giant white building across from the port) and requesting from over there. I kind of hate Boston taxis ....
If you want a table for 2 on the later end (say between 7:45 and 8:30), is it easy to get a reservation? Or should we just sign up for the later fixed seating?
Yes - as @GTJ described. If you were going on Royal out of Cape Liberty (Bayonne), you'd likely be better off going into Newark.
Also, public transit with luggage (even without small children) can be a lot in NYC if you aren't used to taking public transit.
Have you looked to see if transportation from YUL to the port is an option through the cruise line?
I'm doing a Boston to Quebec cruise on Holland, and have booked transport from the ship to YUL through Holland. It was $54 a person, which is much cheaper than basically any other option. Yes, I know it will be a slow bus, but it gets us where we need to be.
Depending on where they are based, getting to Quebec City via air can be very expensive, with terrible connections, versus a direct flight to Montreal.
Not sure when you are arriving, but I would definitely consider changing it - you'll be dealing with rush hour traffic, etc. It's not far from the cruiseport, but in traffic it can take 40 minutes or more.
If you stop in other Canadian ports (Halifax, Sydney, etc.), you'll have already cleared Canadian customs at your first port.
We also have an overnight in Quebec City on Holland America later this summer, so I'm curious as well. I assume it depends on the cruise line and possibly the ship.
I just picked it up for $24.99. As a solo traveler, I think it makes embarkation day a lot easier, and is worth the premium over the wifi package.
But I certainly wouldn't pay the $35.99 it was going for before the most recent sale.
I was not expecting to be as hard as it was - I've done a lot of city driving in San Francisco, Houston, and Boston, and I assumed it would be about the same. It's particularly confusing in Montreal because there are bus lanes that are only bus lanes at certain times, but figuring that out and quickly processing that information in military time while driving wasn't much fun. The second time we went we flew and it was much more relaxing as the public transit is wonderful.