There is only one record that I can see in the Acadian Records of a Thomas born to a Thomas and the timeframe is not correct nor the area.
On the 7th of July 1851 Thomas, age 11, born of the lawful marriage of Thomas McDonald and Alice Welch was baptized. Sponsors Mary Usher and Samuel Murphy. Woodstock RC Parish, New Brunswick.
Again the choices on the 1851 census for a Thomas with a son Thomas are limited. In West Isles, Charlote county you have 86 year old Thomas McDonald, fisherman married to 45 year old Elizabeth with 7 young children. Thomas has just been born.
In Springfield, King County there is Thomas Mcdonald, 65, painter visiting at the home of Abraham Gray.
In Chatham, Northumberland County there is Thos McDonald, 64, farmer with Ellen (55) and children Ellen(24), Margaret(23), John(19), Timothy(16) and Thomas(14). In 1861 the family is still in the same area and Thomas(23) is still with his parents.
Do you know any of the siblings of your Thomas? Finding out his father's name has eliminated possibilities but certainly it would be helpful to have more information.
Debbie