There are trains which run several times a day from Logan to Middlebury. My D & S attended Middlebury Summer Language Academies for a few years; we flew them in and out of Burlington from CA, and didn’t find it noticeably more expensive than flying to Logan. What you may save in $ flying to Logan, you will spend in other modes of transport and the time it takes from Boston to Middlebury.
Also, I know this sounds like crazy town - fly into Montreal and take the bus from there to Middlebury (4.5hrs)