I get the なかなかの策士 part, but what does the first part of the sentence mean?
is used to say "Despite one's appearance", "Contrary to how one looks", "Even though one may look otherwise".
Contrary to how he looks, / He may not look like one, but he is quite a schemer.
こう見えて（も） literally means "Even though (one) looks/appears this way". こう refers to how one looks/appears, and the phrase is used to say that it (= how one looks / one's appearance) doesn't match what one actually is.