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Generally, "ceded" means a cession of territory between legally equal entities. That is not the case here.
What happened in 1664, was that Charles II granted James a colonial charter for New York as a proprietary colony. This was a feudalistic arrangement Charles used to reward his supporters, but also to delegate authority for developing the remote colonies. In a sense, proprietors were like the medieval Marcher Lords of the Welsh border.
Thus, while this instrument invested James with viceregal powers over his possessions, the colony remained under the king's ultimate jurisdiction.
We see from the history of other proprietary colonies demonstrate the supremacy of royal authority. King James issued an order-in-council suspending William Penn's proprietary charter for Pennsylvania in 1692. George I's royal government took over direct rule of Carolina from its Lords Proprietors in 1720. The proprietors were powerful on paper, but derived their powers only from royal authority.