I'd say AAC is better because it is more modern, and is apparently replacing AC3. I always go with AAC anyway. Noting that the AC3 has a higher bitrate, I dont think an extra 64kbps would dramatically change quality.
Both won't make a huge difference in sound, its hard enough in well recorded music, its even harder if not impossible to notice any difference in an anime, TV show or movies, even if you have very good equipments.
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yeah either format is good, but AAC seems to be more common today as it is almost always used with h.264. Anyway its hard to tell the difference, even between AAC and FLAC.