While it's been known that animators at Sunrise are handling the opening movie for the Zone of the Enders HD Edition, the actual PS2 games themselves are not being remastered by Kojima Productions alone, according to Kojima Productions Report #154. A third party is developing ZOE HD alongside the internal team.
Could it be Platinum Games? Some have speculated that it could be Bluepoint, whom we know handled MGS2 & MGS3. However, the fact that KP is actively keeping the developer that they are "closely working with" a secret suggests that it's likely to be a different team altogether.
Note: ZOE HD discussion starts at about 30 minutes into the podcast.