Hello and welcome, KolaKube8!
Do you have Thomas's marriage certificate? It should give his father's name and occupation, as long as he knew them and reported them accurately (and didn't just state "deceased" for instance).
Basic information is useful to start out with.
In 1861, he is in St Anthony (as Clare), in the Coast Guard Service, with wife Elizebeth c1817; they are together (as Clear) in St Keverne in 1851.
Their eldest child is Margaret, born c1843 in Veryan, which is also where Elizabeth was born.
I'm not finding a likely marriage under either version of the surname, but it seems unlikely it would have been before 1837.
Do you know Elizabeth's surname (e.g. from a child's birth certificate), and have you searched for a marriage at FreeBMD?
http://www.freebmd.org.uk/cgi/search.plOh wait, in 1861, Ancestry has inferred her surname from her father in the household: Williams.
So the marriage was 1836 in Kenwyn:
http://www.cornwall-opc-database.org/search-database/more-info/?t=marriages&id=492250Rats.
Oh -- Elizabeth's father was John W Williams, a widower, fisherman, in 1861.
Was this the John Williams whom Philip Clear's widow Julia married??
Julia Clear and John Williams married in Veryan:
http://www.cornwall-opc-database.org/search-database/more-info/?t=marriages&id=771466so it's looking quite likely that the connection you are suggesting is a good one.
In 1841, Julia Williams c1796 Ireland, and husband John, army pensioner c1786 Cornwall, daughter Julia Ann c1821 foreign parts, and Jane Clear Pomeroy, aged 5, "daughter of a ??", are in Veryan.
But oh well -- I would think this is Elizabeth in 1841, mistranscribed at Anc'y as CLOAR, in Veryan (if Thomas was on vessels, I believe he would not have been recorded in 1841), with a different John Williams:
John Williams 55 ag lab
Judith Williams 55
Elizabeth Clear 25 Ind
Philip Clear 4
A different John Williams -- but a strong indication of a connection with Philip Clear, in the name of her son. His 1837 baptism in Veryan:
http://www.cornwall-opc-database.org/search-database/more-info/?t=baptisms&id=1557065showing father Thomas as a shoemaker ...
The data are the same for the baptism of Margaret Williams Clear in Veryan in 1843:
http://www.cornwall-opc-database.org/search-database/more-info/?t=baptisms&id=1557275i.e. residence Portloe, but he is now a mariner.
So ... it looks to me like there is a strong case for the connection, but that's the best can be said from the data to date, I'd say!
oops, cross-posted with claire, but I'll leave this as it fleshes out some of the details a little more.
Even though the two John Williams-s in question are different ones, I wouldn't be surprised if there was a cousinship there, given the names, ages and location.