For the last number of years we buy a nice assortment of seafood in Ingonish at a little seafood market and make seafood chowder at our campsite.
There is a little place right in the town on the same side of the road as the Freshmart (you can easily find this as it is the only 'grocery store' in Ingonish). The place I'm talking about really looks like a large baby barn...small has a nice assortment of fresh fish and seafood and I seem to remember good prices.
You are also really close to Neil's Harbour in Ingonish and I think the co-op there has fresh fish as well (but perhaps things are different this year).
Have a wonderful time, Ingonish and the Cabot trail are lovely!
I live in Cape Breton (not on the trail however) but go there yearly for at least a week of camping. As such we eat most of our meals at the camp site rather than in restaurants, however when a rainy day, or a day trip to the trail beckons, one of my favorite places in Ingonish is the Seagull Restaurant. I'm going to honest and say that the food is only standard but the view is amazing on the deck overlooking Ingonish and the ocean. If you are looking for fish and chips (fresh but deep fried) and want to lounge over the ocean this place is wonderful.
The place mentioned above in Cheticamp is delish...the fish cakes are very very good. Basically if you get seafood any place around the trail you are likely getting local and freshly caught fair.
If you have any questions about the area please feel free to ask me a question or two. I've lived in Cape Breton my entire life which gives you access to 34 years of experience and I'm more than happy to help if I can.