A little confused about timing my train ride from Vernazza to Pisa, then to Pisa Airport

I'd suggest taking the earlier train from Vernazza at 07:12 (arriving 08:44), especially as it's almost an hour shorter in travel time. However you'll have to be quick with the change of trains at La Spezia as it's only a five minute stop. You'll likely have to go down to the transfer tunnels (with luggage) and then back up to your next departure platform. Also, both those trains are Regionale so DON'T forget to validate your tickets prior to boarding the trains on the day of travel or you'll risk hefty fines which will be collected on the spot!

Also, I don't believe the train you suggested will allow you enough time to see the tower (except for a quick glance) and still connect with your flight.

A few other points.....

• What are you going to do with your luggage while you're visiting the Tower? There is a Deposito Bagagli at Pisa Centrale, but if there's a queue it could take some time to both drop-off your luggage as well as retrieve it.
• Given your time constraints, I'd suggest taking a Taxi from Pisa Centrale to the Tower (distance is only ~2.4 kM so it should be cheap). I'm not sure if there will be Taxi's waiting at the Tower, so you may have to either phone them or pre-arrange for a pickup to take you back to the station.
• Take the PisaMover Airport Bus from Pisa Centrale to the airport.

Buon Viaggio!

Thank you so much!

also to save time be aware that you can pay the driver of the bus for your trip from the train station to the airport via pisamover bus, dont get in line at the train station ticket window (biglietteria), if you have some euro's left you can pay as you get on the pisamover. i waited in a long line at the airport ticket window for a pisamover ticket (going the other way than you!) and could have just paid the bus driver. that transfer is really easy.