3 Days in Florence…Day Trip?

When you say three days do you mean four nights? If not, stay in Florence the whole time. If yes, take a direct bus to Siena (1h 15m) for the day.

Lots of museums and churches are open: https://www.visitflorence.com/florence-museums/open-on-mondays.html

My favorites among these, although some may be closed on the Monday you are in Florence since some alternate, are:

Palazzo Davanzati

Opera del Duomo

Brancacci Chapel

Bardini

San Marco

Chapel of the Magi (by Benozzo Gozzoli)

Bargello

Will arrive in Florence in the morning on Sunday and leaving on Wednesday

There's enough to fill a week in Florence.

Open on Mondays:
-The Opera del Duomo Museum - the new Duomo museum is excellent BTW.
-Pitti Palace and Boboli Gardens
-Bargello Museum
along with many, many churches.

But a trip to Siena is never wasted - it's up to you.

Buy tickets ahead of time for things you really want to see and have a great trip!
=Tod

You have so little time for Florence that I'd just stay in the city unless you are not interested in what it has to offer.

Virtually all of the duomo sites are open on Mondays.
https://duomo.firenze.it/en/home#times

The Bargello is open on the 1st and 3rd Monday of a month.

San Marco is open the 1st and 3rd Monday of a month

Cappelle Medicee is open on Mondays.

Check the visiting hours for the museums listed above on the b-ticket site for the Florentine State Museums:
https://www.b-ticket.com/b-ticket/uffizi/default_eng.aspx.html

The Church of Santa Croce is open on Mondays:
https://www.santacroceopera.it/en/organise-your-visit/#opening-times

The ancient and very important church of San Miniato is open on Mondays:
Monday-Saturday 9:30-13:00; 15:00-19:00
https://www.sanminiatoalmonte.it/contatti/

There's likely more but you see? There's no reason to leave Florence on a Monday just because some of the museums are closed! :O)

No one mentioned my favorite: Basilica Santo Spirito. I believe it was also designed by Brunelleschi, and the artwork was so beautiful. It is one of the few places where you cannot take photos. It was closed our last day there (Wed), so I didn't get to go back. The Bargello is totally worth it, but be warned that their combo ticket isn't a good deal if you cannot fit in all of the remaining museums in your limited time there. We also got into the Medici Chapel, but the Palazzo Davanzati had odd hours we kept missing when we were there, Casa Martelli is only open Saturday, and Orsanmichele wasn't open at all (even though it was supposed to be and said it would be on its website). It was 21 euros w/ the service fee (even on-site), and in early March there were no lines for either of the places we visited. Be warned that Sunday is a zoo in Florence. Mon-Wednesday were amazing in contrast!

As a side note to the cupola of the Duomo in Florence, we picked a timed slot on a Sunday at 3:45pm, and it was great. Cruise-goers were starting to leave, and we were able to walk straight into Giotto's bell tower and climb an hour before our cupola climb. The ticket guy kept saying we were crazy to do both so close together, but it was fine for my teen and me. There was strangely a lot of line cutting for people whose timed entrances were nearing. Most of the Americans just let everyone with a nearer ticket time go ahead of them, and we all made it in eventually. Keep that ticket out (or your phone charged) as you will need it at least twice. This is common to show it to pass through security, then scan it later in the queue for almost all of the museums in Italy.