You can get the tourist boat or the local supply boat from San Stefanos harbour, neither operate daily but run frequently throughout the week.
I recommend going on the supply boat just as we did if you like the traditional side of things, its packed with food and consumables for the island and is hardly modern but nonetheless great fun and you have a good chance of being the only passengers besides the local crew.
We didn't actually go to Mathraki but Erikousa (Wednesdays) which is a little farther out being the most northern point of Greece, you can see it from San Stef not sure about Arillas. The fare there was 7€ per person each way and took about an hour, about half way into the trip the crew told us to go sit outside which we did to be greeted by a family of Dolphins jumping in and out of the water and guiding the boat, I think there war about four of them. My Mum was awestruck and I only realised when retuning how rare it is to see them like that in the wild, many locals have never seen them, if we had been on the Tourist boat we would probably have missed them.
Erikousa had the most amazing beach and water, so still and clear and even has a small reef which is great for snorkeling, it looks like they had just finished building a very nice hotel
www.hotelerikousa.gr which I had lunch at and can recommend. The island made Arillas look built up so if you really want to get away from it all this is perfect, there is even a very modern looking Heli Pad on the island so starting to wonder at what type of holidaymakers they are targeting, if you fancy a climb you can walk up to it. Click on the link the helipad is just below the second 'o' in Hotel Erikousa on the front page.
I would love to spend a chilled out week on this island.