Hello kzichelle, with two nights just arriving off the plane I think Isola d'Elba is probably ambitious and would involve a lot of logistics to get there and back just to them move onto Siena.
The beach areas south of the Arno (which flows from Pisa to the coast) and Livorno are essentially a long strip of beach lifestyle coastline and I'm sure some people with more experience will chime in about them. But would also recommend looking into the southern shore of the bay of La Spezia. It features beaches, rocky coastline and larger and smaller towns to choose from. Some place like San Terenzo has beaches and is adjacent to Lerici if you want something bigger or Tellaro if you want a Cinque Terre like town without any tourists.
It would be about an hour by train (Pisa to La Spezia) and then a bus or taxi ride to the town itself. This seems like a more manageable travel plan than Pisa to Piombino to a boat to Isola d'Elba or whatever that transport plan is. Especially then having to reverse it and then onto Siena a couple of days later.
My $.02, two extra days seems like a great problem to have, enjoy,
=Tod