You may wish to check out my website http://www.buckhoutfamily.com
While still a work in progress there is much there that you may find helpful. As far as I am aware, Capt. John (Johannes) Buckhout's father was Matthys Buckhout. I'm assuming you mean the one b. abt 1682 and d. 1785 in Westchester Co., NY.
However, am always interested in new research that proves new information, so please feel free to let me know! Not sure who the Isaac Buckhout is that you are referencing.