Hmm... that would depend on 2 things for me:
1. Transportation: If you have a car then transportation isn't a big deal, but if you don't have a a car getting there in the morning from another resort you will need to give yourself at least 1hr for travel.
2. Food preference: Breakfast food is generally a pretty standard fare, so if you're thinking of a more exotic/adventurous variety I suggest trying for dinner. Don't get me wrong I love both offerings (I will do both on our next trip ) but if it's your first time I think dinner is a better option.
I would go for dinner. After a busy day in the park it will be nice to just relax at Boma for a wonderful dinner. If you have never been to the AKL make sure you take the time to explore the resort. It is such a beautiful resort. Boma is a very good place for dinner. We have eaten there twice and enjoyed it both times.
Boma for dinner is better than Boma for breakfast. Like cseca said, breakfast is rather ordinary fare, but dinner is very good. And you don't want to pass up the soup or desserts.
If you are going by bus, I don't think it matters whether you are going for breakfast or dinner as you'll have to transfer somewhere at some point to get back to WL.
I enjoy both beakfast and dinner at Boma but as virtually everyone has pointed out, dinner really has more unique choices. Breakfast is kind of a standard american style breakfast with a few unique items tossed in (Quinoa, Pap, some breakfast casseroles). I go to Boma for dinner on EVERY trip but only occassionally do the breakfast (and I often stay at AKL so the transportation isn't an issue). I recommened both meals, but if you are choosing one, go with dinner.