Whats the best approach for converting EyeTV captures for Media Player playback?

Over the holidays I’m going to finally get to capturing many of our old VHS tapes and put them on my NAS for accessing from Media Player.  So far its working very well, but I’m not totally happy with the quality when using EyeTV’s export to “Apple TV HD” option.  For anyone else that has done this, what is the best way to re-encode the files for playback on the Apple TV using Media Player.  I’m willing to have the files be a lot bigger if the quality will be better.  I realize that I’m working with crappy source, but I want to shoot for the best quality output. 

Is there some process or settings that would yield better playback quality?  Thanks.