Hi Eleri,
I'm assuming that you don't have the 1861 for the family as you mention not having found John in 1861.
1861 Census Llanllyfni
Ty'n Fawnog
Catherine Rowlands, head, 29, widow, Farming 6 Acre Farm, Llanllyfni
John, son, 3, Llanllyfni
Richard, son, 1, Llanllyfni
Griffith Pickards, boarder, 24, State Quarrier, Llanllyfni
David Jones, boarder, 22, State Quarry, Blacksmith Journeyman, Aberffraw Anglesey
RG9/4336
Folio: 82
page: 18
Regards
Darcy