Hmm how long have you had him? As in how use to flakes is he? I had this problem with a fantail once and switched to sinking pellets which to start off with I use to make sure I'd drop them right in front of him. It didn't take him too long to catch on and then he loved the sinking pellets. But I imagine it depends on the fish. Maybe try that out But also try feeding other foods that sink such as peas. They are a bit bigger than pellets so he might notice them more. Though make sure you use normal frozen peas with no added salt or anything. Then just de-shell them and break them up into bits. My fish loves peas and they sink as said.

I had a similar problem, not with swim bladder issues as a consequence though

But they will get used to it eventually, besides, goldfish usually dig around on the bottom for food, so after a few days, he should notice that the goodies are on the bottom and not the top anymore You could try feeding him shelled and thawed peas for a while, they're bigger and have a strong green color that he should notice

They like most veggies and fruit And also different kinds of live foods! For now, I'm feeding mine with freeze-dried blood worms and tubifex, which they love There's also spirulina, krill and other things available Both freeze-dried and simply frozen. It's an awesome way to vary the diet of your goldfish, and he'll grow even bigger and more beautiful that way
So for veggies, I've given mine cucumber, peas and lettuce, but you could also try with boiled carrot or potato, as long as there are no spices! You could try some banana, strawberries, watermelon or the pulp of oranges But be careful with the more juicy things, they might disturb your water quality unless you remove the leftovers after a couple of hours