We've eaten at both many times and really like each. Personally, if I had to choose, I would go Biergarten however. First, being in Epcot, you don't spend a lot of time traveling to get to dinner. (It can take a fair amount of time to get over to AKL even if you have your own car.)
Second, I like the entertainment offered as part of the Biergarten experience. The band that plays is really fun!
Third, being of Polish heritage, I find the German food is an opportunity to get some familiar favorites I don't make too often at home - like some varieties of kraut, the different sausages, etc.
Lastly, the beer in the Biergarten is better plus you get to sing "Ein Prosit" with your stein in hand - not something I get to do at home either.
The food at Boma's is great, but for me it lacks the extras that make Biergarten the easy choice.