Not sure if you're aware... but there's actually a street in the north east end of Scarborough (now Toronto) called John Stoner.
I'm not sure whereabouts he would be buried.There are numerous cemeteries in Scarborough but there's only a few near the street which I assume was named after the John Stoner you've inquired about.I don't know the names but there is a church cemetery near the Toronto Zoo which is quite old.It's on Finch Avenue, west of Meadowvale.There's also an older cemetery on Markham Road just north of Sheppard Ave. There isn't many stones in that cemetery and there's a lot of development going on around it.
You might be best to contact the Scarborough Archives for assistance on this.It's quite possible they will know more about his burial.
6282 Kingston Road Highland Creek (Scarborough), Ontario M1C 1K9