Andrew- I'm hoping you still check this board. Your data sounds pretty similar to my own story.You do not give any dates, though, so it's hard to tell.
My great-great grandmother was named Maria Quinn and she was born in Ireland and immigrated to the US with her family sometime prior to 1846. Her father's name was James Quinn, her mother's name unknown.
My Maria Quinn had a brother named John Joseph Quinn and he was born in NY about 1846 [est. from 1880 Brooklyn, NY census where we see him working as a machinist]. He was married to a Louise Maria Bergen who was born about 1848 in NY and the 1880 census says that both her parents were also born in NY. Children for them that I know of so far: Clara Quinn b. abt. 1874 NY [assume Brooklyn], John Quinn b June 18, 1877 Brooklyn, NY [seen as "Joseph" Quinn on the 1880 census with his parents, living on Montgomery St in Brooklyn, NY], and Catherine Quinn b Sept 1879 in NY [assume Brooklyn]. I also know of one other son, Thomas Quinn born Sept 1884, NY.
Both John Quinn [Jr] and his brother Thomas Quinn were living with my gg-grandparents, Maria [Quinn] Flynn & her husband James Flynn, also an Irish immigrant on the 1900 census for Brooklyn, NY. The relationship given for the Quinn boys was nephew.
Maria Quinn and her brother John Joseph Quinn also had a sister named Margaret Quinn b. abt 1839 in Ireland. We see her living with my gg-gp in 1860 in Brooklyn, NY and Margaret was working as a seamstress then. There may have been other siblings but I have not found them yet. Still having trouble finding the father James Quinn on the 1850 census.
Well, let me know if you think there's any possible connection here.