Thomas and family can be found in Penrhyndeudraeth in the 1891 Census too
RG12: 4644; Folio 119; Page 21
Tyn y Ffrwd, Llanfihangel y traethau (this is the parish that includes most of Penrhyndeudraeth)
Thomas Owen head 44 Quarryman born Mochdre Denbighshire
Jane Owen Wife 39 born Penrhyn Merioneth
Richard Owen Son 12 ditto
Wm Owen Son 8 ditto
Mary Owen Dau 4 months ditto
THOMAS OWEN son
10 ditto
Ellen Pugh Sister in Law and visitor 50 Single born Penrhyn
Given that Thomas is still 10 in the 1901 Census and that Mary is 14 by then I suspect that the "months" should belong to Thomas and not her. As the census was taken on 5th April 1891, that would suggest that Thomas was born in May / June 1890.
The unmarried sister in law has the surname Pugh. This suggests that Mrs Owen(s) may also have been a maiden Pugh.
With all this information the Ardudwy district registrar should be able to give you an exact date and place of birth.
See this URL for contact details:
http://www.gwynedd.gov.uk/gwy_doc.asp?cat=3440&doc=9413