You might want to check this record and follow up here. Just a Thomas Mooney in PA that could be the father. I would build Wikitree profiles for all of the Thomas Mooney's in PA. Then follow each of them. It will take a while, but it will be rewarding when you find the right one.
I haven't checked yet, but there also seems to be mention of him being from Maryland. Unfortunately it adds more work, but it could be why it is so hard to find him.
"United States Census, 1820," database with images, FamilySearch (https://familysearch.org/pal:/MM9.3.1/TH-1942-25122-45293-61?cc=1803955 : accessed 16 May 2016), Pennsylvania > Greene > Franklin > image 2 of 6; citing NARA microfilm publication M33, (Washington D.C.: National Archives and Records Administration, n.d.).
I created a profile for him and his family here Mooney-1154 and built up his FamilySearch record here https://familysearch.org/tree/#view=ancestor§ion=details&person=LD51-VPH.
Date of Death: 14 Mar 1896
Subject: Thomas Henry Mooney
Source: Holt County Sentinel, 27 Mar 1896, p. 4
Died, at his residence in Savannah on Saturday, March 14, 1896, Mr. Thomas Henry Mooney, aged 70 years, 2 months and 22 days. Deceased was born in Lancaster, Pa., December 21, 1816, was married to Caroline Harris in Clark county, Indiana, in 1844 [sic]. Ten children were born to them, nine of whom are still living. Deceased has lived in and near Savannah since 1877. The funeral took place on Monday, conducted by Rev. A. J. Brock.-- Savannah Reporter.
Mrs. J. W. Baker, of this city, was a daughter of the deceased, and was in attendance at his bedside during his sickness and also there in attendance at the funeral.