Our 2 favorite breakfast choices so it depends on whether you want a buffet or want to be served. Both have interesting menu choices - Kona has the more traditional choices, Boma has the usual familiar breakfast foods and additional offerings with African overtones.
If I had to choose just one I would pick Boma because there is a larger selection of dishes with interesting flavors, and the opportunity to explore AKL and go outside afterwards to see the animals.