Hi Edd
We did it about 3 years ago.Just go to one of the ticket agents around Samos town harbour.It does work out cheaper but dont forget you have to pay a 'port tax' on top.
You get picked up right outside Kusadasi Harbour with a Turkish guide.
You spend the day with the guide which is brilliant.
But beware our guide told us that as part of the tour we would be stopping off at a carpet shop near the harbour to see how hand made carpets are made.Facinating to learn how they are made BUT then the salesmen appear from nowhere and will not take no for an answer.
I had to give him a wallop and then his mate when he pulled a knife out.
Dont let this put you off though,just dont go in to the carpet shops.
Have a walk round the bazaar instead and pick up a bargain or two.