Yep, Machado does have a higher career WAR...and SS/3B > Outfielder.
But Harper has one "Daaaaaaamn, he did THAT!" season, and as good as Manny is, Manny hasn't done that. IMO, if Harper gets more than Manny just did, it's cause a team is gambling on him for 3 or 4 more of those types of seasons. That's why these two are so valuable, it's rare to see guys this young hit the FA market BEFORE hitting their primes.
Ultimately, I agree with you, Machado has had a more valuable career thus far. I think that Harper shoe has to drop by Friday at this point.