Florence Conundrum

1. Arrange for late check-in with Cinque Terre hotel

or

1. Skip the Leaning Tower. Honestly seeing a decent video of it will suffice.

I would say skip Pisa. It is a fun place to go if you are in the area and have the time. The leaning tower is neat but no big deal compared to CT. Also very crowded with lots of bus tours and all you see in that area is the tower and booths selling stuff. The town of Pisa is suppose to be great, but not where the tower is and you would need extra time to spend it in the town.

I would try to change the check-in time. It is very unusual to be so early and I wonder if there was a language issue and it was meant to say after 4 pm?

Personally, Pisa took my breath away. Not because of the leaning power but because of the incredible sight of the entire "Field of Miracles" as a whole. However, I wouldn't stop there for just a few minutes to take a photo of the leaning tower. If you really can't change your check-in time in Vernazza, skip Pisa. Maybe you can have a stop there after your visit to CT?

I agree. I would double, triple check the check-in time. In all of our travels we have never encountered a check in time before 4 pm. It is always stated as after 3, or 4 pm. However, it using something like AirBnB or an apartment then it is possible that the owner has to leave by 4pm.

I'm guessing your specific check-in cutoff is because you rented an apartment? If that's the case, I'd go along with skipping Pisa as well.

Yeah, I would be emailing with your Vernazza accommodations. I've never heard of having to check in before 4, with no flexibility. What if it was your first day in country and your flight had been delayed?

Even a small, one-room operation can make late check-in arrangements for you. As an AirBnB host myself, I like to greet new guest and show them around (offering early check-in when possible), but if they won't get into town until after 21:00,... I'm leaving a key under the mat for them.

If you're renting an apartment and were requested to be there by not later than 4pm, and you're not there, you don't know whether you possibly will be scrambling around for a place to sleep in the CT that night (which could be a problem at the last minute any time after May). An apartment is not going to have continuous or 24/7 reception like a hotel would.
For European travel, KISS, Keep It Simple.

If you will be in Firenze long enough, you could daytrip to Pisa in half a day.

isabel,

I've encountered the 16:00 check-in rule in the Cinque Terre in the past. I suspect the owners have specific hours-of-business so want clients to check-in by a set time, as they want to go home and have dinner with their families.

I agree with the others, and in that situation I'd suggest continuing with the Accademia tour as planned, but skip the Pisa visit. IMO, your time would be better spent in the C.T.