MiLB.com has a quote from Paul dePodesta about each guy which makes the whole thing well worth reading.
So, for fun, lets compare MiLB.com's list to say, the best Mets' prospect at each position in my estimation.
[sny-table rowheader=true columnheader=true]
C;Kevin Plawecki;Kevin Plawecki
1B ;Allan Dykstra;Dominic Smith
2B;Wilmer Flores;Flores or Dilson Herrera
3B ;Zach Lutz;Lutz or Aderlin Rodriguez
SS ;Wilfredo Tovar;Amed Rosario
OF;Travis Taijeron;Cesar Puello
OF;Cesar Puello;Brandon Nimmo
OF;Dustin Lawley;Champ Stuart
RHP Starter;Rafael Montero;Noah Syndergaard
RHP Starter (Honorable Mention);Gabriel Ynoa;Ynoa or Montero
LHP Starter;Steven Matz;Steven Matz
Reliever;Jeff Walters;Jeff Walters
C: Travis d'Arnaud has prospect eligibility, but given that he will start 2014 in the big leagues, for the purposes of the minor league system, Plawecki is pretty clearly the top catcher.
3B: This is probably the weakest position in the Mets' minor league system. I know that David Wright is the Mets' best player, but the system is really thin at third.
SS: Any Gavin Cecchini fans out there can argue he is the top SS prospect and not Rosario.
OF: Puello and Nimmo are pretty clearly the top two outfielders. After that, it's really a matter of preference. If you want some big league value, Cory Vaughn and Darell Ceciliani will both play in the big leagues, but do not look likely to be starters. I'm very intrigued by Ivan Wilson and Champ Stuart from the 2013 draft class. Stuart has the tools to play center - he's really fast and has a plus arm - so that moves him ahead of Wilson for now.
Reliever: Walters is probably the best relief prospect working as a reliever, given that Familia has too much big league time to qualify as a "prospect" and other guys who I view as relief prospects like Jacob deGrom (probably), Cory Mazzoni, Erik Goeddel, Logan Verrett and Domingo Tapia are all still starters.