At the moment, the buses from the Pisa airport to Florence and the train take roughly about the same time, but I believe it is more convenient to just take the bus directly from the airport. Both arrive at the same train station (SMN) so there isn't difference there, but if you take the train, you do need to go to Pisa Centrale, change trains and then move on to Florence. I'd choose the train option only if the bus schedule is not convenient to when you arrive.
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