You mentioned that you were not sure if the Thomas Cromwell, witness to Prudence Cromwell's marriage was a brother or a father.
There is a birth record in the Drouin Collection
Samuel, son of Thomas Cromwell, farmer of the parish of St. Sylvester and of Margaret his wife was born on the second day of April and was baptized on the sixteenth day of the same month in the year of our lord one thousand eight hundred and forty-four in the presence of the subscribing witnesses.
Thomas Campbell, Minister
From this I would think it likely that Thomas Cromwell was her brother unless her father was still having children at that time.
I see that you have access to the Drouin Collection so won't copy here all of the entries I found but will list them for you. All are births of children of Thomas Cromwell
Samuel above as well as
Richard son of Thomas Cromwell and Margaret Clements - Dec. 27, 1851, baptized March 25, 1853
Robert, son of Thomas Cromwell and Margaret Clemins - Oct. 17, 1854 baptized Nov. 21, 1854
Alexander, son of Thomas Cromwell and Margaret - June 15, 1856 baptized July 2, 1856
I did not find a marriage for Thomas and Margaret though.
I took a look at the 1851 census for Quebec and found Thomas and Margaret and family.
1851 ST. SYLVESTRE, LOTBINIERE, QUEBEC
Thomas , farmer, age 38 bon Ireland, protestant
Margaret Clemens, age 35, born Ireland, protestant
Thomas, age 19 born St. Sylvestre, Protestant
James, age 17 born St. Sylvestre Protestant
Margaret, age 15, born St. Sylvestre, Protestant
Pruddy, age 13, born St. Sylvestre, Protestant
Samuel, age 11 born St. Sylvestre, Protestant
William, age 9 born St. Sylvestre, Protestant
Elizabeth, age 7 born St. Sylvestre, Protestant
Sarah, age 2 born St, Sylvestre, Protestant
Albert, age 1, born St. Sylvestre, Protestant
After seeing the 1851 census I went back to the Drouin and found births: St Sylvestre
James born Sept. 1, 1834 son of Thomas and Margaret (although Margarets names looks like Walla?
Prudence born May 15, 1840 daughter of Thomas Cromwell and wife Margaret
Richard, born April 25, 1842 son of Thomas Cromwell and wife Margaret (I wonder if this was a son who died as they had another Richard born later)
Margaret , born Sept. 21, 1836 daughter of Thomas Cromwell and wife Margaret
** Yes, Richard did die - I found his death record
Richard, son of Thomas Cromwell of St. Sylvester died 22 of Dec. and was buried 24 of Dec. 1846.
Elizabeth, daughter of Thomas Cromwell and wife Margaret Clements - Jan. 12, 1848
both Thomas and wife Margaret have signed (this one is odd though as Elizabeth is 7 years old in 1851 census so should be born about 1854 rather than 1848?)
Sarah, daughter of Thomas Cromwell and Margaret Clemence his wife - April 7, 1850
I did not find a birth for Albert
I also found them in 1861 and can copy for you if you would like me to. In this one I see that Elizabeth is 12 which matches with birth record so looks like 1851 was just wrong.