Well besides the huge difference in one being a buffet and the other being a signature dining restaurant at Disney, the differences between the two:
1. Atmosphere. Jiko is upscale, has a wine room with a huge selection of Afican wines, is dark, intimate, mainly adult only dining. Food is supherb in both preparation and presentation. Although the appetizers are very unique, the entrees are standard fare, short ribs, filet mignon, etc. Dining here is leisurely, our last meal in January took 2 hours.
2. Variety. Boma offers to much more choices and although there are several dishes that are not "extreme" this place does offer quite a few African themed dishes, more than Jiko does. It provides the opportunity to experiment; you can get a spoonful of something and if you don't like it, you can just not eat it and can return to the buffet tables for something else.
We love both of these places. I would pick Jiko everytime for a dinner with just DH and I or with friends. I would pick BOMA everytime if it's a family meal.