In the current absence parish records online, a possible line of enquiry for you would be Griffiths Valuation. This was a land taxation survey carrieid out in Ireland between to 1850s and 60s. This show details on land holdings for those people included, and lists basic details on the land and types of buildings involved. Only heads of households are included, with no personal details, but the results can give possible locations to follow up.
the database is available to search on AskAboutIreland at :
Griffiths ValuationThere are a few James Flynn's listed in Co. Waterford - including one in Dungarvan - see : Griffiths search -
James Flynn, Co. Waterford His entry is dated 1851. Do you have any clues as to James' occupation or trade ?
other than that all I can suggest is to double check records at your end to see if anything shows a more detailed location and then keep an eye out on the IrishGenealgy website (and RootsChat) for any news on Waterford records.
Shane