I'm sorry to say, I'm not sure that there is really a good option available. The challenge of puffins + mobility challenges is a hard one.
We were all over the west coast of Ireland, from Galway, the Aran islands, the Cliffs of Moher, all 'round the Dingle Peninsula, out to Great Blasket Island, Velentia Island, Portmagee, and yes, out to the Skelligs, around the ROK. Never saw a single puffin in any of those places, including way, way out from civilization. Except in one place, where we saw thousands of them, up close, in-your-face-close: that was climbing up Skellig Michael. They were everywhere (have a look), but definitely not a place for the mobility-challenged.
Here are a couple earlier threads that discussed the challenges of western Ireland for someone with mobility issues which you might find useful:
West Ireland sights for seniors
Puffins on Inishmore?
The short version is, this is not going to be easy, may not be possible at all.
The only place I've seen even more puffins was in the Faroe Islands (on Mykines), but that was no easy, level stroll either (maybe not quite as dangerous as climbing Skellig Michael, but not safer by much).
We're skipping Cliffs of Moher
Actually, the COM are the one place were folks with mobility challenges will be able to easily and safely get right up to the edge of a good cliff in western Ireland. It's perfect for that, in fact that's what it was built for. If they want cliffs, this is the place to go. Easy, safe, level, paved paths right up to the very stout barrier right on the cliff edge, you can't fall over the edge even if you tried very hard.
getting out of the boat at Skellig Michael would not be an option for
her.
Having done it myself, I wouldn't say that getting out of the boat at Skellig Michael is any more of a challenge than getting on (or of) of the boat anywhere (including the dock at Portmagee). They do have non-landing trips on the same boats which circle Little Skellig (right next door to Skellig Michael). There are countless sea birds on that island (perhaps millions? hard to count..), if you take that boat trip, do NOT forget a good "rain hat" or jacket with a waterproof hood (not because of rain, but because of...blessings from above). Most of the birds there were gannets, as I recall we did see an occasional puffin go scooting by, but they were not close. If your partner could manage getting in/out of the boat at the dock in Portmagee, one of the non-landing trips out to Little Skellig would get them close, probably close enough to see a few puffins fly by, but not close enough to lock eyes with them.
Alas, I do not know of a good, reliable accessible place to see puffins. I've seen them once in a while from the deck of ferries in the Canadian Maritime provinces, and in Alaska. No guarantees, you need to get lucky - but at least those decks are fairly accessible.
