Tomoyo After is absolutely not part of the CLANNAD series. Its characters are quite distinct from the ones in CLANNAD, it has a different writer, different artist… The only thing it shares is names. You could argue a similar case for Kud Wafter. You can call them spin-offs, but they are very much different series’. Rewrite Harvest festa! is a fandisc of Rewrite; it is part of the Rewrite series, and doesn’t aim to be anything different. The same applies to Little Busters! EX. You’ll find this logic is consistent throughout our Series Information pages as well.
This is a really bad way to determine your favourite. You can’t say “X is my favourite even though it isn’t out yet!”. Base your judgement on what you HAVE read instead. Does the existing Angel Beats! media stand above everything else Key has produced for you?