Checking the 1861 census of NB, I see a Joseph Thompson and family living in St. François parish in New Brunswick:
Joseph, 45, Anglican religion, b. in NB
Jane, wife, 23, b. in Quebec, Anglican
Joseph, son, 4, b. in NB
Marey, daughter 2, b. in NB
Next door is this family:
William Thompson, 48, b. in NB, Anglican
Rity Thompson, wife, 31, b. in Quebec, Anglican
George, son, 9, b. in NB
Mary, daughter, 7
Gabey, daughter, 4
Arline, daughter, 2
Next door:
Eliza Thompson, male, head of household, 35, b. in NB, Roman Catholic (name might actually be Elija)
Lucey, wife, 30, b. in Quebec, Catholic
Daniel, son, 9, b in NB
Leonore, daughter 8
Peater, son, 5
Peney, daughter, 3
James, son, 2
This is all on pages 3-4 of St. Francis parish, 1861 (not online).
This family is in St. François in the 1851 census here:
http://www.upperstjohn.com/1851/stf6.htm#19, you probably have already found them. It seems they stayed in the same place over that decade, so pretty safe to put place of birth St. Francois parish (at that time it was Victoria County, Madawaska County broke away only decades later).
Here's info from the 1871 New Brunswick census (also not online):
St. Francois parish, p.72:
Joseph Thompson, 58, b in NB, Roman Catholic, French, farmer
Jane, 32, b in NB, Roman Catholic
Joseph, 12
Betcey, 11
John, 9
[start of p.73]
Maryann, 7
Peter, 6
Dulfis, 4
Andrew, 5 months
Here are other Thompson families in the same place, also page 73:
Charles Thompson, 54, b in NB, Roman Catholic, French, Farmer
Maryann, 34, b in NB, RC
John, 15
Henry, 12
Catherine, 10
Mary Ann, 7
Hiram, 6
Jane, 2
William Thompson, 66, b in NB, RC
Locad, 40, b in NB, RC
Andre, male, 15
Maryann, 14
Talli, female, 13 [probably Nathalie]
Adeline, 6
William, 2
Checking the marriages in New Brunswick (which have been published) I don't see any of these couples marriages recorded there.
What's interesting is if you check the 1851 census (p.19, line 15) you see Joseph Thompson, age 34, living with Edward, age 8 (presumably his son), and the remarks column says "
wife left him." So the marriage in 1856 was a second one, though it's this fact wasn't noted in the parish register, usually it is. That earlier marriage did not take place in any of the Catholic churches in the St.John valley in New Brunswick.
Joseph Thompson born about 1817 had other brothers in the area: Charles, Elijah Ludger, and William.
Those are the ones listed in the census. Their father was Pierre, who had died by the 1856 wedding of Joseph.
Also, do you know what it means on the baptism records for St. Luce when it says: depuis 14 jors, or depuis 2 mois?
At the top of each record there is a link to the main page which gives translations. In this case:
hier = yesterday
avant hier = day before yesterday
depuis x jours = x days ago
depuis x semaines, mois, ans = x weeks, months, years ago
So
depuis 14 jours means 14 days ago,
depuis 2 mois means 2 months ago.