Although he married twice, he had no children and wished to found a school of science where students could help facilitate many of New England's new industries. With Ichabod Washburn's input, they decided to form a school which combined practical experience and academics. Boynton donated $100,000 anonymously and died before the first school buildings were completed.

Boynton is memorialized in Boynton Hall (1867), Boynton Street (on faculty row), The Peddler (the class book at WPI), Boynton Library