The majority of museums are either closed Sunday OR Monday, not both days. That way they alternate and on either day you'll find something open. The major ones open on Sundays and closed on Mondays are the Uffizi Gallery and the Accademia Gallery. So you can definitely plan your trip to visit those on Sunday and then visit others on Monday - here is a list of the Florence museums open on Monday.
If you're interested in a specific museum, make sure to check the Florence Museums page and check individual opening times and closed dates. There are a few that are closed on Tuesday - the Bargello museum, which is mainly sculpture and which I personally really like, is one that comes to mind. Also there are several that alternate closing on Sundays or Mondays depending on the week of the month - check the San Marco museum's hours to see what I mean
If you're interested in a specific museum and times don't seem clear, just ask and we'll try to help sort it out! Hope you enjoy your 3 days in Florence