If you use iTunes for both library management and playback, you need to stick with AIFF. iTunes cannot play FLAC files.
If you are willing to use a 3rd party playback software, then FLAC is the way to go for storage and ease of use. Both Audirvana + and Pure Music use iTunes for library management, even though iTunes isn't acutally the playback software. They do this by creating "pointer files" (my term) that look as if they're in iTunes but actually reside on your HD.
This would be my preferred route if using a Mac.
If you are willing to use a 3rd party playback software, then FLAC is the way to go for storage and ease of use. Both Audirvana + and Pure Music use iTunes for library management, even though iTunes isn't acutally the playback software. They do this by creating "pointer files" (my term) that look as if they're in iTunes but actually reside on your HD.
This would be my preferred route if using a Mac.