I also am researching Brubakers in York County PA.My connection is through my grandfather, Erastus J. B. Brubaker, born in York County around 1888.His father was Jacob H. Brubaker and his mother was Magdalena Cassel, both of York County.
My records for the 1860 census show Andrew Brubaker (born 1832) at age 27 in Lower Windsor Township of York County, living as a laborer in the household of Samuel Brubaker, age 39 (c/b 29), a farm laborer, and his wife Mary H., age 28, and their children Mary Jane (7), Clara A. (4), and Lorencia [?] (1).
Just two names down there appears to be a second Samuel Brubaker, age 22, a farmer, and his wife Rebecca, age 18, son Milton (3) and twins Eliza Jane and Mary Ann (7 mos.).
Also in the 1860 census for York County is another Andrew Brubaker, age 57 and hus wife Leanah - in Manchester Township.There are additional York County Brubakers in this census also: Elizabeth (33), Alfred (7), Samuel (8), Anna M. (6), Henry (29), Susuan (26), Amanda (4), Emma C. (1 month), Susan (38), Elizabeth (30), J.C. (42), Martha (42), Emma (19), Elizabeth (16), George (11), Mary (7), and Sally (3).