They are both excellent in their own way. It depends on the mood you are in. Boma is louder, has more families and a more energetic atmosphere, and of course, it is a buffet so you will be getting up and down a lot during your meal. If you are in the mood for a more energetic restaurant and to try lots of different types of foods, I'd say go to Boma.
Jiko is very quiet, relaxing (very few children are usually found here) and is more of a place you would go for a relaxing or romantic meal. I'd say if you are going to be tired after visiting the parks, and would prefer to have someone bring you food rather than you keep getting up for more, go to Jiko. You can't lose either way!