One possible reason might be the New Englanders did not always view the Native Americans as legitimate candidates for conversion. There certainly were missionaries in New England who converted Native Americans into so-called “praying Indians” (see the thewampanoag.com source given below for a brief overview), but their efforts may not seem as systematic as those in another part of the so-called New-World. The Spanish influence over what would later become the southwestern United States seems to have focused pretty systematically on the conversion of the Native American whereas the northeastern colonists seem to have been focused more on uneasy coexistence and gradual displacement. The nebraskastudies.org source cited below presents a third possible reason: “the Native Americans generally didn't feel that they needed to be saved.”
Mary Rowlandson’s famous account of being captured and held for ransom by Native Americans may say a great deal about how the New Englanders tended to view the indigenous people. She admits that there are a few “praying Indians,” for example (during her trying experience, she even secures a copy of the bible from one such person), but on the whole she describes the people whom she encounters as “hell hounds” and as the willing servants of Satan.
There are no doubt a number of possible reasons to suggest. I hope this answer gets you moving in the right direction.