There are obviously slight differences in quality across the Skellig boat fleet but, apart from, say, the Skellig Walker, which offers the option to sit inside the cabin, the differences are not that meaningful. To put it bluntly, the quality of the boat is entirely secondary to the primary concern which is, do they have free spaces for the date you want? Any boat that can carry you to Skellig Michael is a good boat, under the current circumstances. Plenty of people would go out in a leaky bathtub if it guaranteed that they could set foot on the island.
Either of the two options you mentioned are fine. All boats meet a minimum standard to do the trip so I wouldn't worry too much about this. Just pick one and go with it.