I have been to both and love them equally, but they are very different.
Boma is a family friendly buffet; the food is interesting (and very good); and service completely self paced. Be careful of the desserts, many of them have alcohol (they are marked, so read the cards). I love going to this restaurant with my kids; they get to eat quickly, and love going back to the buffet and trying new things- everyone loved the carrot soup and the hummus.
Jiko is a much more upscale, romantic dinner spot. Although children are, of course, allowed- the restaurant decor is more subdued, the room is quieter, there are usually more courses involved - and the flavors are more complex; the wine list is extensive, and the service is fabulous.
If you only have time for one meal, I would examine what you think your family would enjoy more. Personally, I would feel stressed with my little ones at Jiko, but can relax with them at Boma- and after we walk around the grounds and enjoy the atmosphere with them. But what is best for you is really based on your family. Trust me, neither is a "bad" choice.