Considering:
1) Wikitree's name guidelines say: "We aim to use the names that people themselves would have known and that would have been recognized in their own time and place";
2) that the sources above all seem to agree, at least in part, that Rathbun was in common usage at the time John was living, (while Rathbone was more common both a few generations earlier and a few later); and,
3) the closest thing to a primary source (i.e. the epitaphs of other family members) use Rathbun.
I would suggest Rathbun should be used unless other evidence can be found that indicates Rathbone was actually used for this individual during his life.