Two very different restaurants. I like them both.
If I had to choose, and I had not been to either, I would choose BOMA because it is an incredible experience, lots of really good food, and in a beautiful hotel and atmosphere.
Capt Jacks, I tried in Sept for the first time and I've been going to Disney a long time. Great dinner and I'm going back in Sept, but I could probably get that same dinner/atmosphere a million places.
BOMA, again, truly a new adventure and I think everyone should go at least once. Food for even the basic foodies, but lots of neat things to try, and yummy desserts. Schedule in time to enjoy the hotel lobby, animals etc too !