I am not sure I understand whether you will be moving around solely with public transport or have your own car while in Italy:
How many days total were you planning in Tuscany, 5 days? Did you already exclude Porto Ercole completely? If you love the sea and being in nature, I highly recommend spending your 5 days in Tuscany at the island of Elba. Lots of beautiful crystal clear water, both sandy and pebbly beaches, with lots of walking trails in the hills above for a bit of hiking.We were going to go to Port Ercole/Il Pelicano but since we have excluded Rome, we don't feel like driving.
You didn't say when you're coming but since you want waterfront I am assuming you are coming in the summer months. Elba can get a bit crowded then but it is still beautiful. Here are just a few choices for resorts in Elba to start your search!