Thanks for all of the replies!
The informant on the death certificate was his wife Mary who it seems should be a relatively good source for his parents' names.
John Henry Fagan married Mary Louise Fitzsimmons in New York City in 1878 as aghadowey discovered in the NYC marriage indexes. No parents are listed on the marriage cert for either of them and they definitely moved in with the bride's family after the birth of their first son so her parents were known but for whatever reason not listed on the marriage certificate.
Their children were named (in order):
- John H(enry?) Fagan - Born 1878
- Nanette C Fagan - Born 1880
- James J Fagan - Born 1882 (my G-Grandfather)
I have found him and his wife in the following censuses (with occupations listed):
1880 US - Manhattan - Waiter in Hotel - Living with wife's family and young son John
1900 US - Manhattan - Engineer, Stationary - Living with wife, 3 kids, and daughter Nanette's child John
1910 US - Mamaroneck, Westchester (outside NYC) - Engineer, Stationary - John and Wife living with Nanette and her husband.
1915 US - Mamaroneck, Westchester (outside NYC) - Gardener - John and Wife living with Nanette and her husband.
1920 US - Manhattan - Engineer, Machine Works - living only with wife Mary back in the city.
1925 NY - Manhattan - Engineer - with wife and son James J who seems to have split with his second "wife" (my G-Grandma)
1930 US - Mamaroneck - Retired Engineer - Back in Mamaroneck living near daughter Nanette.
My G-GF James was a bit of a drifter/womanizer it seems and disappeared from his family when the kids were young and so the Irish part of my verbal heritage was essentially lost. I've tried tracing the side branches down further to see if I can find any other living relations down other lines but so far no luck.