I see EqG as canon too. There's really nothing in the series to contradict that (and I remember statements by the show crew that implied so). I'll add Flash Sentry to the list of things the two have in common – he had a couple of appearances in FIM after his debut in EqG.
EqG works either way - if you want it to be canon, that's fine - nothing in FiM contradicts it. If you don't, well, nothing in FiM specifically points to it either.
It also doesn't have to be FiM canon to enjoy it. Of course, Nightmare Rarity is neither EqG canon OR FiM canon :)