One way to see Ephesus is with a ship’s tour but it is not cheap. The best way is to get on the net and arrange for a guide who will arrange the taxi and take you through and explain everything. You can negotiate for a taxi to take you to the starting point and meet you at the other end. Sometimes they will provide a guide and sometimes it is possible to "acquire" one at the start of Ephesus. Some people use a taxi then wait for a passing tour and latch onto it and piggyback their way through. Certainly it is a tour you should do one way or another, it's fabulous in the literal sense. Whichever enjoy ... Neil .
You can get to Athens easily enough from Piraeus so that wouldn't be a problem. I'm not sure how easy it is to get to Ephesus from Kusadasi? You may need to get a taxi and I'm not sure how much that would cost, but if you do that, agree a price in advance, and negotiate!
One point to bear in mind is that we did an excursion to Ephesus a few years ago, but went to several other places as well which you probably couldn't do on your own, plus we had a brilliant guide, which is also something you'd not get going on your own.
The other warning I always give is that if you go on an excursion from the ship, and get held up, it's their responsibility to get you back on board, if you go on your own and get held up it's your responsibility, and the ship won't wait for you!
We got back from this cruise last Friday and had a brilliant time (see my review) and I'm sure you will too :-).