Keith Law has posted his 2011 MLB organizational rankings at ESPN (subscription required), and the Mets rank 26th overall.
26. New York Mets
Earth to Fred Wilpon: This is what a strict adherence to slot recommendations will buy you. Parsimony has its price.
The Braves are ranked 3rd, Phillies are ranked 5th, and the Yankees are ranked 9th, so the Mets' chief divisional and geographical rivals have all done a better job stocking their farms with talent and depth. Law doesn't go into detail about most teams so it isn't clear if he has excluded guys like Josh Thole, Dillon Gee, or Fernando Martinez. Not that there's a likely superstar among them, but I'd expect the system to rank higher than 26th if any or all of them were included in the group.
Ike Davis and Jon Niese are recent graduates of the Mets farm system, which doesn't excuse the organizational lack of succeeding prospects in their place, but it should be a credit to the Mets for having developed them in the last few years.