Milan, Como and Cinque Terre in 4.5 days?

If the Last Supper is a 'must do', I would decide on either CT or Lake Como. Trying to do both has you mostly on trains the whole time.

Do the Milan days at the end.

You "could" but that's a lot of traveling in very short period of time. Most people here would likely encourage picking between Como or CT, but not both. Save visiting Milan for the end.

Unfortunately, you’d be on trains for four hours each way to the Cinque Terre and you’d need to stay a couple nights to make it worth your while, as the journey to get there is unremarkable.
From Milan, you could overnight on Lake Como in the town of Varenna. Then, continue up to Tirano, Italy to take the train route of the Bernina Express. The halfway point is at Pontresina/St.Moritz Switzerland. It’s a train ride widely considered to be one of the world’s most spectacular.

I’ll offer a couple of recommendations:

In Milan, you can walk on the rooftop of the Duomo. That was a really neat experience for us. We were the first handful of people up there and getting there early made a big difference.

In Varenna on Lake Como, our Rick Steves My Way tour stayed at the Villa Cipressi. This was a beautiful hotel with lovely gardens on site. We also enjoyed a small yacht tour of Lake Como, including a tour of Villa Balbianello.

I agree with others that trying to do Cinque Terre along with your other plans would be a lot of travel and not much time to relax.

Laurie

If going to Milan, Lake Como, & the Cinque Terre means just checking off places to visit on some bucket list, 4.5 days could do it.

Otherwise, I would never, ever do this. For 4.5 days, pick just one.

We will be taking the train. If we visit Lake Como, should we stay in Como or Bellagio or somewhere else?

Como is a city, not at all like the smaller towns most people want to see. The mid-lake area seems most picturesque and has very good ferry service. Popular towns there are Varenna, Bellagio and Menaggio. Of the three, only Varenna has a train connection to Como (and thus to Milan). For the others, you'd take a train to Como and then a ferry, bus or private transportation onward.

Lake Como is a popular topic here. You can use the Search function to find earlier threads on the topic, some of which will include hotel recommendations. This is getting fairly late to be booking lodging for April, so you may need to do some preliminary searching on booking.com to identify places with vacancies on the nights you need.

Lake Como threads from the most recent two years

Would it be a good idea to stay in Como and take the Ferry to Bellagio for the day?

What type of experience are you looking for?

Como is a city with all the amenities.
Bellagio is a beautiful town with upscale shopping and restaurants.
Varenna is a charming village with lovely views and only an hour by train from Milan and easy ferry to Bellagio and Menaggio.

On our first trip to Lake Como, we took the train from Milan to Como city and then the ferry to Bellagio. That was magnificent. It’s not the most direct route, but the journey was part of the experience. I think we returned to Milan by train from Varenna. I would recommend that and staying in the mid-lake area. Have a wonderful trip.