I think Charlie’s right about the major hashkafic difference between YCT and JTS — JTS faculty held clearly non-Orthodox beliefs (such as Biblical criticism and the rejection of Oral-Torah-from-Mount-Sinai) by early in the 20th century, and by the 50s they were doing such things as issuing statements annulling all kohanim marriage restrictions. In contrast, neither YCT nor its faculty hold any clearly non-Orthodox beliefs. Its students are required to daven at a shul with a mechitza, which hopefully should keep out the Conservadox.
However, I did notice on their alumni page that a few of the YCT alumni have gotten master’s degrees at or otherwise studied at JTS. I’m not sure whether it was before or after they went to YCT — I guess that makes a big difference.