have a look at this thread:
As Cristina said, I sugget you contact the farmhouse owner directly to be sure there are farm animals.
The last one, Le Casine di Castello, offers several activites for children to discover farm animals: ask them if they are dedicated to the farmhouse guests only or if your children can partecipate also.
It is located about an hour and a half driving distance from Florence, amidst the marvellous countryside of Valdorcia.
Agriturismo La Ripa, set in the Mugello valley north of Florence, seems to be the right solution for you: it's closer then the first one and also offers educational alctivities with animals for children, as well as the Agriturismo Palazzo Vecchio.
However, I strongly suggest you to verify the possibility to take part in the activities: just email them and explain your needs and what would you like your children to explore and see in a real working Tuscan farm!