Would love some suggestions on the best way to get to Cinque Terre from Florence. Where is the bestbplacevto stay for 2 nights? We have 5 days after that to explore before leaving from Milan back home. Any suggestions.

For your transportation options, see rome2rio.com

For a recent (days old) thread on where to stay in the Cinque Terre, see
where to stay Cinque Terre

We took the train from Florence with a change in Pisa.

Well it's about 3 hours by train - via yes a change in Pisa Centrale and usually La Spezia to any of the five Cinque Terre Lands or villages - these are mainly regional trains where it is best just to buy tickets at station day of travel - dirt-cheap flat fare - check Acquista il biglietto con le nostre offerte - Trenitalia for schedules and fares; for lots on Italian trains also check www.seat61.com; BETS-European Rail Experts and www.ricksteves.com.

You may want to head then to Lake Como or Lake Maggiore for some days after and before leaving from Milan - you can easily go from either lake to Malpensa Airport without going thru Milan. Milan however is a fascinating city too so I'd spend the day before flight there for your last supper!