Okay - this will probably only frustrate you (!) but I looked up Mattie Penney in the 1900 census.There she is, in Omaha, Ward 2, Douglas County, NE!!!But Thomas isn't with her!!!
She's listed as "Head" - b. March 1870 in Ohio.Both her parents were born in Virginia.She is married, for 12 years, and bore 2 children, 1 of whom was still living.
With her is the living child ... Harry Thomas, b. July 1891 in Nebraska.
I then looked at all 12 of the Thomas Penneys in 1900.Only one was born in 1861 ... I found him listed as a patient in a hospital in Worcester, Massachusetts.It says he was born in Canada to Canadian parents and emigrated to US in 1862.(And, of course, Toronto is just above Ohio...???!!!)But it lists him as Single ... could be a mistake, or this simply isn't your Thomas.
Anyway - hope that at least the Mattie Penney info helps. Best, India