As far as I know Assassin is a super-set of Ninja: I think they can do/learn everything a Ninja can and a bit more. So no reason to wait with changing really.
The only thing you might consider is to make another character Assassin: if you e.g. switch a paladin to assassin (OK, not the best role-playing choice perhaps) he gains more new skills/traits than if you switch a ninja.
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