Dan Szymborski of ESPN, who created the ZiPS projection system examined Keith Law's Top 100 MLB prospects through a Zippy lens.
For anyone who care about process in analyzing minor league players, go read the whole thing.
If all you care about is Mets showing up on lists, well, there's that too. Law is higher on a few Mets than ZiPS. The first is Dominic Smith, who Law had ranked #37. ZiPS just doesn't have much to say about a guy who played only a handful of games in rookie ball as Smith did. The Nationals' Lucas Giolito falls in the same class.
As for the bigger actual disagreement, it's on Travis d'Arnaud who ZiPS ranks #86 and Law #36. Szymborski writes:
After two years filled with injuries, ZiPS sees d'Arnaud as too risky to put anywhere near the top 50. Catching is a physically demanding position, full of disappointing catchers with offensive potential who just stall (Ben Davis, Ben Petrick, Javier Valentin, etc.) and d'Arnaud has lost a lot of valuable developmental time. He turns 25 next week, so that time is hard to get back.