There's really only one person this could go to. And it's Boston College running back Andre Williams.
Williams was nominated for the Heisman Trophy, he won the Doak Walker award for best RB in the country, was a unanimous All-American, unanimous All-ACC, and he set school and ACC records for rushing yards in a season with 2,102. So yeah, the best college athlete in New England. Without a doubt.
Give an honorable mention to BC hockey forward Johnny Gaudreau, UMass-Lowell goalie Connor Hellebuyck, Chaz Williams and Cady Lalanne from UMass basketball, and UConn basketball's Shabazz Napier.