Staying in 2 bases over a 6-day stay will prevent you from spending a large part of your days driving.
In my opinion 3 days in Nafplio is the right choice if you want to visit the city, Mycenae, Epidaurus and the surrounding area.
If you feel fit enough to drive 2 hours to Nafplio after a long flight, the drive from the airport is easy. It's up to you...
Close to Nafplio, to spend a few hours on a beach, without too many crowds, there is a nice little village nearby: Candia
https://maps.app.goo.gl/Gvau35UjiFbUhsMe9
Messinia is a splendid region.
I don't know where exactly you plan to stay in Costa Navarino If your thing is modern resorts with international standards like The Westin Resort, this is probably the place where you will find what you need.
Personally, I avoid this kind of place at all costs to feel that I am really in Greece, and I would prefer Marathopoli or indeed Pylos which have more charm. But it's your vacation and your tastes. not mine.
As a castle guy, a few minutes south of Pylos, also see Methoni and Modon Castle
And don't miss the archaeological site of Messene which is just as impressive as Olympia.