I'm afraid the answer might well be that you can't find ferries between Naxos and Samos because there aren't any.
Now the whole ferry service from the mainland and Cyclades to Samos, Chios and Lesvos is in the melting pot because of the seemingly unstoppable collapse of NEL Lines. As a result summer times are nowhere near being agreed. It is possible there may be connections at Syros or Mykonos if none of the Piraeus-Samos ferries stop at Naxos.
www.gtp.gr will show you times that exist as they are released, but you'll need to work out connections yourself. Allow PLENTY of time....