Lodging Rome for 2 nights

For accommodations try using booking.com for starters. You can zero in on the location, price, etc. and they do include apartments.
Or do the same with airbnb.com. Last year, we stayed in Monti in an airbnb.
Last time we were at the Vatican, (2018) we had to snake our way through a very long line to get to the Sistine Chapel, and it was extremely crowded inside. And there was a definite feeling of being rushed through, hardly any time at all to appreciate the place. (Completely unlike my first visit in the 70's when my friend and I were the only ones inside and could sit and stare up to our heart's content)
So....with only one day, I'd go for St. Peter's....you can wander at your own pace, spread out and marvel at the Pieta, the Baldichino and all the sheer splendor. I don't know if you can still walk up to the cupola or not, but if so, that's a fun trek up with a fabulous view.

https://search.ricksteves.com/?button=&date_range=1y&filter=Travel+Forum&query=Rome+hotel+&utf8=%E2%9C%93

The more important question may be how are you arriving to Rome and how do you intend to get to your cruise port? You will have to deal with luggage in that case, which you won't have on you visit to the Vatican/ St. Peter's.

For a short stay, I would suggest a hotel over an apartment - too much "overhead" involved with the latter. I found that you can end up working around the host's schedule rather than you own.

Since these are your “must see sights”, be sure to be on top of when ticketing opens for the Vatican museums and have a plan in place.

Thank you, I have changed to a hotel. Casa White. I have not figured out how to get from hotel to ship.

That hotel is not anywhere near the Vatican
You’ll need to use public transportation or a taxi

Your previous post
https://community.ricksteves.com/travel-forum/italy/sistine-chapel-or-st-peters-basilica-b8ac4016-5193-4bc7-9b80-48c679cf9abf