Are the 2 segments on the same ticket so that Amtrak is guaranteeing the connection? Is your train from Boston an Acela? Normally, Amtrak does not guarantee connections that tight. However, since there is only one train between NY and Florida daily, things may be different.
Only the Silver Star is running now and it connects with very few trains. On the other hand, the Silver Meteor, which may not start running again until 10/3, connects with many trains. I, personnaly, had to change a reservation and spend the night in NYC in order to get to Chicago in early October because the expected return of the Silver Meteor was delayed until after the date of my reservation.