4 Nights in Florence is really just 3 full days plus a few hours the day you arrive, so if you take 2 days trips, all you have left for Florence is only a day and maybe a half day on the day of arrival, depending on when you arrive.
Having said that, the best (fastest as well as cheapest) way to get to the Cinque Terre is by train. It's not a short trip since it involves at least 2 trains if not 3.
You can see your options by going to the train company website:
www.trenitalia.com
Enter from: FIRENZE TUTTE LE STAZIONI (Florence all Stations) (Note A).
To: NAME OF VILLAGE (Note B)
(A) For departure station you should select all Stations in Florence, rather than only Santa Maria Novella (the main station), because there are fast trains that go there and which call only at the FIRENZE CAMPO DI MARTE station (Florence 2nd largest). The train departing from there is a FrecciaBianca, a high speed train, which departs early in the morning, but gets you to your destination faster (you will need to change to a regional train at La Spezia, the city just before the Cinque Terre.
(B) As the name implies (Cinque means 5 in Italian), there are five villages you can choose, from East to West: Riomaggiore, Manarola, Corniglia, Vernazza, Monterosso. All of the 5 have a train station. The largest village (and the one with most trains, including faster Intercity) is Monterosso, which is the furthest to the west. The most visited is Vernazza (the village before Monterosso).
I have no tour companies to suggest for the Chianti area.