We've been to Boma twice (Sept 06 and Jan 08) and Tusker House once (Jan 08) and both were great for us. We are vegetarians and DH is a marathoner with a huge appetite and there was plenty of delicious food for him at both (still lots of stuff for the meat eaters too!) The food isn't the same, but both places offer dishes that are influenced by African and Asian cuisine, while still catering to kids and the meat and potatoes crowd. Both also had many selections, so you could try a little bit of many things, and then really dig into something you love.
If you only plan to do one of them, I think it comes down to how the places fit into your larger plan. Animal Kingdom Lodge is awesome, so if you want to take some extra time to check out the lodge and maybe listen to the storytelling they do every night or take a look at the animals, you could make a whole evening of it. And the atmosphere of Boma is really neat too.
Tusker House isn't quite as cool, but it is very relaxing and casual. When we were there, it seemed like it hadn't really been discovered yet. We walked right in without ADRs and it wasn't nearly as crowded as Boma. Plus, it is very easy to fit into your Animal Kingdom visit and is definitely the best place to eat at that park.
Both have delicious desserts in those lovely tiny portions so you can take lots of different ones, and go back for seconds, and pretend you aren't being a pig (or a Pooh.)
In our experience you can't go wrong either way. Have fun!