John arrived in New York on 13 June 1862 via the ship Manchester, traveling with his wife, Jane Prior Thomson, their two children, James, Lois. Also married son, John Thomson, Jr. his wife, Sarah Simmons, and their children, Christopher John, Edna Agnes and Orson Spencer listed separately in ship's log.
The roster for the James Brown company (where the surname is spelled Thompson) indicates that John was traveling with his "family." The family sailed to America in 1862 on the ship Manchester.