First of all, there are no graves at Mount Vernon that I know of. There is a family tomb in which various members of the Washington and Custis families are entombed. If you are referring to Confederate aide-de-camp John Augustine Washington III, the last private owner of the estate, and the one who sold it to the Mount Vernon Ladies' Association in the 1850s, he is neither buried nor interred there. He was killed in action at Cheat Mountain, [West] Virginia on September 17, 1862, and is buried in Charleston, WV. The obelisk in front of the family tomb bearing his name is simply a monument to him and does not indicate his reposing on the Mount Vernon grounds.
...and one of his wife's kids married Lee.
No, Martha Washington's grandson, George Washington Parke Custis, married Mary Lee Fitzhugh, and of course are the parents of Mary Anna Randolph Custis, the eventual wife of Robert E. Lee.