You could use any of those options. 'Better' is the most general, whereas 'recharged' and 'refreshed' speak more to your energy level and mood/state of mind.

You can swap "refreshed" with "better" or "recharged" in that sentence. "Better" just means you feel generally improved. "Recharged" is like saying you got your energy back. So your sentence could be: "I was tired after the long flight, but I felt better after sleeping at the hotel." or "I was tired after the long flight, but I felt recharged after sleeping at the hotel."