"Niles" may have an older connection to "Knell" in Old English, but there does seem to be a bit of confusion regarding the John who immigrated to Massachusetts in the first place.
There was a certain John Knill who immigrated from Wales and came on board the ship, "Speedwell." But our John Nile/Niles/Nyle most likely arrived from Dorset-shire (probably Beaminster). There was a large group of emigrants who left this area of England around the same time because of the economy and the failing reign of King Charles. And they moved to Dorchester. John Niles' children bear a great similarity in their names to the Nile/Nyle families of Beaminster, Dorset, particularly the family of John Nyle and Johane Paviot who did have a son named John born about the same time as ours who settled in Braintree.