Louisa died in 1901 after having lived in Victoria for 47 years which indicates that she must have also migrated in 1853 or 1854.
John & Louisa married in Oct 1853 in England, so we know they were in England at this time. 
Their eldest son Thomas is born on 11 Jan 1855 in Waugh Terrace, Bourke Street, Melbourne, Victoria, Australia.
They must have migrated shortly afterwards perhaps on the Mary Stoddart which sailed in April 1854 with only a small number of passengers including a Mr & Mrs Williamson (unfortunately first names and ages not listed).
This is the only possible match that I have been able to find for the couple, the entry reads as follows:
WILLIAMSON ---- MR A
WILLIAMSON ---- MRS A
It appears that they were travelling with no children and were both over 21. (Note the “A” stands for adult not their first initial). 
Anon., 'SHIPPING INTELLIGENCE' The Argus, 3 April 1854, p.4 . Retrieved December 2, 2016, from http://nla.gov.au/nla.news-article4805280
There is no Louisa listed on the incoming passenger list at all in either the assisted or unassisted passenger lists for incoming shipping to Victoria in from 1853 to Jan 1855 time period.
Has anyone else found them? I'm desperately looking for help, any ideas of where to look next would be wonderful.
LinksTo learn more about John & Louisa Williamson click here
Sources Death certificate of John Williamson, died 7 Jun 1874, Registrar of Birth, Death and Marriages, Victoria 6427/1874
 Death Certificate Louisa Williamson, died 6 Sep 1901, Registrar of Birth, Death and Marriages, Victoria, 9613/1901
 Marriage certificate of John Williamson & Louisa Walker married 10 October 1853, General Register Office, England, Dec quarter 1853, Shoreditch registration district, 1c/364/311
 Birth certificate of Thomas Williamson, born 11 Jan 1855, Registrar of Birth, Death and Marriages, Victoria, 218/1855
 Taken from the Index of Inward Passenger Lists for British and Foreign Ports 1852-1899, MARY STODDART B 066 001.