I don't think there's any research comparing nattokinase to Eliquis, so there's no way for a layman to make that comparison. I don't think trying to compare them is even wise.
Without question, if I needed an anticoagulant, I wouldn't risk using something that has very little research behind it. How much is enough? How much is too much? What's the half-life so I know how often to take it? Does it address the types of clots I'm trying to prevent (legs vs atria vs valves, etc)? Is it a little bit effective, a lot effective, or not effective at all? What other foods, supplements and medications does it interact with? Does it work the same in an 80-year old as it does a 60-year old?
I don't know the answers to those questions and don't know anyone who does, so I would never take that risk.