There is a Nathaniel Thomas Niles (born bet. 1821 & 1825)who was baptized with his siblings at the Church of Notre Dame on 1 Mar 1825 in Montreal, Quebec, Canada. The record names his parents as Nathaniel (b c1786 RI- d alive 1850 Acadia, NY) and Mary (Herrington) Niles (b c1782 NY - alive 1850). I have their ancestry which traces to RI & Mass for Nathl and to NY for Mary.
I don't have any further records for their son Nathaniel Thomas Niles, who he married, etc. His name though is very similar to your Thomas Nathaniel Niles who was born at the about the same time.Is there is a d/rec for your Thomas Nathl Niles in Canada that lists his parents? Canadian census records indicate Thomas as born in England, but that could simply have been the census taker's assumption.
One of Nathl Thomas Niles' brothers was named Ephraim Cone Niles (born Greenbush NY). A son of your Thomas Nathl Niles' is named Wm Cane Niles.Their middle names are very close in spelling.
A death record for your Thomas Nathl Niles might name his parents and his actual place of birth. You have his wife as Lucy. Would you have her surname, place of birth, and when they married?On the surface it seems improbable that they are the same person unless he returned to Canada (to Ontario) as an adult from the US after, say 1840. The parents of Nathl Thomas Niles were in the US again at Hancock, Mass, for the 1830 US census.