Organizational farm system rankings are a tricky thing. On one hand, they're completely subjective. Organizing them is basically guesswork. On the other hand though, for a reputable site, a ranking can combine quantitative evidence, scouting reports, thoughts from executives and scouts, and expert opinions from analysts and prospect writers. As far as prospects go, that amount of information is rare and should at least be considered.
"Jorge Mateo, Aaron Judge and Gary Sanchez make up a core of promising position player prospects that any of the organizations above would love. All three have the potential to be regular Major League contributors and possess the individual tools (Mateo with speed, Judge with power, Sanchez with his arm) to become stars. What the Yankees lack is pitching. New York believes it took a potential leader in James Kaprielian out of UCLA with their pick at 16th overall last season, but there isn't much more pitching in the system beyond Domingo Acevedo, who could rocket up the rankings if he can expand his repertoire beyond a 100-mph heater."
It's not that far off from most opinions this offseason, and on most accounts I would agree. The Yankees saw their system contribute to the major league team significantly last year, as Luis Severino, Greg Bird, and John Ryan Murphy all established themselves at the big league level. Unfortunately, though, they didn't see as much talent infused into the system as they saw leave it; they drafted James Kaprielian, but that's about it.
In one sense, this ranking is largely arbitrary. While I completely get the methodology behind "graduating" top prospects, those players don't go away. So as far as young talent goes, the Yankees really only improved. They now have Severino, Bird, Starlin Castro, Didi Gregorius, Nathan Eovaldi, Aaron Hicks, Aaron Judge, and Jorge Mateo--all are 26 or younger. They now add Kaprielian, who could make a big league impact within this calendar year, and Gary Sanchez took a major step in moving closer to major league ready.
So, yes, this is not a top ten system. They do not have a Corey Seager or a Lucas Giolito, but they have several players who could be big league contributors, and a bevy of fringe talent that could fill in as fourth/fifth outfielders or utility men. There is certainly a lot that can be improved, but this system is satisfying. Combine that with the young talent on the 25-man roster and you have yourself, generally, a more sustainable group than just a few years ago.