Which would be the most logical choice and easiest to get to after a long plane ride?
How are you going to travel?
Pick the place you want to go to first.
In reality, it won't make that much difference.
The Pisa airport has train station on site. If choose to go to florence first you'll probably take a 5 minute train ride to Pisa Centrale station change trains there and in about an hour you're in florence.
If you choose the CT, you'll pick a train to La Spezia and then change to a local to the CT. Probably about 45 minutes longer trip with an extra train change. not that big a deal.
I assume you're continuing your trip after Cinque Terre and Florence. Since travel connections from Florence to the rest of Italy are excellent, I'd do Cinque Terre first and then Florence. Cinque Terre is also a very relaxing place to begin your vacation.