Which method would result in higher quality?

I have a large video/animation I want to export from AE. Should I export via the Quicktime Animation codec and compress to H.264 afterwards via handbreak, or would exporting directly as H.264 yield better results?
In the case of the former: can anyone recommend the best settings which preserve the quality of the original codec?

Don't export from AE as H.264. The Adobe Media Encoder (and probably Handbrake) will get you better results. Does Handbrake do multipass encoding?
Your composition should already be matching the settings of your footage (in most cases).
The animation codec is mathematically lossless. This means that every single pixel is the exact same once rendered as it was in the AE composition. If you took that file and rendered it again as the animation codec, it would still be the same. No matter how many generations you go through, there will never be quality loss because it is lossless. This is why lossless codecs are ideal for intermediate files.
Another good intermediate codec is Quicktime with the PNG codec. At high quality settings, it is also mathematically lossless, but in many cases the file size is smaller than the Animation codec.

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