The only record I have found so far for John Thomas, son of Lee R. and Helen (True) Thomas, is the 1880 US Census record for the family; I have not yet located and reviewed a record for them from the 1890 US Census. By 1900, the household consists of Lee and Helen and sons Charles (b. 1878) and Arthur (b. 1880). There are only nineteen months between the births of Charles and Arthur, so it's entirely possible that another brother was born in between them and who didn't survive until 1900, but it would make the schedule relatively tight. It's also possible, if the 1880 census listing for the household was recorded in late April or later of that year, that the son John (transcribed as age "0" on the index) was actually Arthur, and his name was changed at some point along the way (or that the census taker simply got the name wrong).
I've not located a burial site for a John Thomas that would fit this description as of yet.