While I don't have any specific evidence to support the claim, the individual that sold me the color model sheet said that it was attributed to Frank Thomas. The story (as it was told to me) is that Frank became ill while he was working on the sequence and Hook's character reflected Frank's feelings.
Captain Hook Color Model Sheet (Attributed to Frank Thomas)
The cel of Captain Hook had a great facial expression, although I wasn't crazy about the hand position. The background was painted by a Disney Studio artist and adds some depth to the image.
Cel of Captain Hook
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From “Peter Pan” (1953). A very large color model sheet of Captain Hook with his hat on. #87 on sketch. Hot water bottle on hat. Attributed to Frank Thomas. Frank is said to become sick while working on this scene (he got into the character). [Image: 15-1/16"W x 11-3/4"H. Frame: 17.25"W x 23-13/16"H] Acquired 1989. SeqID-0103 8/3/2005
From “Peter Pan” (1953). Cel of Hook on his boat with island on a painted master background. [Image: 8-13/16"W x 8-3/16"H] Acquired 1998. SeqID-0329