I believe that your Thomas's mother was Christian/a Rutherford, and that these are the children on the 1891 census:
HENDERSON, THOMAS MMN: RUTHERFORD 1878 S Quarter in STOCKTON Vol 10A Page 73
HENDERSON, MARGARET HELEN MMN: RUTHERFORD 1882 S Quarter in GATESHEAD 10A/857
There is a marriage in 1872 in Rothbury of a William Henderson, and on the same page is Christian Rutherford.
A Thomas Henderson with father Henderson & mother Rutherford died in Sacramento, California on 8 Feb 1953. His DoB is given as 27 Jul 1878, which fits with the above birth record.