Traveling to Skellig Islands

Hi Ashley, is there no possibility you could rent a car? That would be way easier and cheaper for you. Pick one up in Galway and drop it off in Shannon. Or take the bus to Shannon airport and pick up and drop off the car there.
The public transport option is going to involve a lot of changes and headaches that might cause stress to what should be an enjoyable journey. At the same time its doable and could be part of the adventure of getting to Skellig Michael.
My advice would be to rent the car, or secure the services of a private guide who would pick you up in Galway and take you to Portage and collect you there again and back to Shannon. Theres tons of good driver-guides who could do this for you, thought it would be the more expensive option.
Slainte/Health
Stephen McPhilemy
Ireland Tour-Guide

Unless you're willing to rent a car the transportation challenge will be truly daunting, as per Stephen.
Without knowing what your tour may already cover I might suggest that there are options closer to Galway that would be a better use of your time and much less stressful to get to: the ferry out to the Aran Islands (from either Rossaveel or Doolin) is an obvious choice, or maybe the scenic drive along the N59 loop around Connemara to include a stop in Clifden and the Sky Road, with perhaps a visit to the National Park along the way. Returning via the village of Cong would make for a very pleasant (and very relaxing) day out for your final day in Ireland.

Thank you both for the feedback. I think we would feel more comfortable looking into using a private guide. Are there any particular guides you would recommend, or a search site to find contact information for guides?

Here's a link for "Things to do" in Limerick that includes several tour companies operating from the city:
http://www.tripadvisor.com/Attractions-g186619-Activities-County_Limerick.html
One of them may be able to customize a tour for you down to Portmagee, and may even include transport out to Shannon Airport on the morning of your departure. For the 3 of you it might actually be quite cost-effective, and would certainly be the most comfortable and least stressful way to go.
You'd just need to get yourselves from Galway down to Limerick to set things in motion.

Take public bus Galway to Killarney about 4 to 5 hours 1 bus change in Limerick
https://national.buseireann.ie

From Killarney get a day trip to Skellig

http://walkwithme.ie/tour/tour-skellig-rocks-valentia-island/

Get bus from Killarney to Shannon
or ask Tour companies in Killarney if they are going to Shannon early morning to collect some arriving tourists

Ashley,
I'd suggest emailing Tony McGann (who we hired as a private driver two years ago, and recommended him to friends who hired him just a few months ago....they were also delighted with him).

He can be reached by email: tonyscabdoolin@eircom.net

He drives a nice VW van, is very reliable, fairly priced, and has a great personality. He'll (as the Irish say) "look after you."

In fact, our friends enjoyed him so much, they offered a spare condo they have for him to visit Nashville during his recent visit to the US. He was just here last month, and we had the pleasure of hosting him (along with our friends) for dinner at our home.

If he is already booked for when you need him, he can recommend other reliable drivers, too.

You'll love Ireland!!

You'll love Ireland.