Once you get to Samos, Patmos is very easy to get to. Hydrofoils run often depending on season and weather. We actually had a fishing boat take us over when we were staying in Marathokampu Bay. He had been giving us lifts to beaches that could only be reached by boat or goat when he heard us talking about it and made the offer. Heck you could see Patmos from our hotel room. From there we moved on to Rhodes.
Ok this is killing me. I know it's not as cheap as it use to be but now I'm wanting to get back. It's been 3 years since our last trip and the introduction of the euro nearly killed our budget for that run. Next time we will probably stick to the north eastern islands and the Turkish coast and see how that works out.