The Smith family arrived in New York on 5 July 1866 via the ship American Congress. Though the overland company records only list heads of household, it also notes that John purchased 8 adult food rations for the journey indicating that his family was with him for this part of the journey as well.
Her surname is "Ledingham" on the death certificate and "Dilley" on Find A Grave website.
Mary was not on the passenger list for the American Congress with her husband and step-children, unless she is listed under her maiden name and they married either at sea or shortly after reaching the states. However, the records for the Thompson company show that her husband purchased 4 1/2 adult food rations for the overland journey, indicating she was with the family for this part of the journey at least.