John Sickels just released his preliminary Top 20 Mets Prospects, which now gives us a trio of reputable prospect rankings which also includes lists from Baseball America and Baseball Prospectus. Here are the results, with raw average rankings and overall ranks.
Since the three lists were all of different lengths (Sickels had 20; BPro had 11; BA had 10), I shrunk the overall list to only include players who appeared on at least two of the individual lists. This excluded the vast majority of Sickels's 11-20. If a player wasn't ranked on a particular list (e.g. Nick Evans, Ike Davis and Scott Moviel), he received a '13', which appears in the table above in italics to indicate that it's an artificial ranking.
What's fascinating to me is how similar these three lists are. It took only twelve players to complete everyone's top ten, with Martinez-Flores-Niese coming in 1-2-3 overall. Sickels's was the only list to flip Martinez and Flores, preferring Flores's apparent higher ceiling. Also noteworthy is that three of the top five and four of the top seven prospects were international signees, without whom the Mets' farm system would surely rank among the worst in baseball instead of the middle of the pack.