The third of the four daughters of Jeanne (née Ragsdale) and Robert W. Boynton, Sandra was born in Orange, New Jersey, and grew up in the Mount Airy section of Philadelphia, Pennsylvania. Her father was a noted progressive educator, scholar (collaborating on textbooks with Shakespearean scholar Maynard Mack), and publisher and co-founder of Boynton/Cook Publishers, now owned by Heinemann.
Boynton's parents became Quakers when she was two years old. From kindergarten through 12th grade, she and her sisters attended Germantown Friends School, where their father taught English and was Head of the Upper School. Boynton has frequently cited as central to her own "upbeat offbeat" sensibility Germantown Friends’ arts-centered curriculum, as well as its thorough integration of the values of pacifism, independent inquiry, and individualism. She also spent part of her 10th grade year at Ackworth School near Pontefract, England.
She went on to Yale, entering in 1970 in the college's second year of coeducation. She spent the second semester of her junior year studying in Paris through Wesleyan University's program. At Yale, she majored in English, and also sang sporadically with the Yale Glee Club; she had joined the Glee Club when additional singers were needed for a performance of Beethoven's Ninth Symphony at Carnegie Hall, under the direction of Leopold Stokowski. Boynton has described herself as "an enthusiastic but undistinguished alto". At her graduation from Yale in 1974, she received a Special Master's Magna solemnly bestowed by Charles Davis, the Master of Boynton's residential college, Calhoun College. Unbeknownst to the graduation audience, the honor was actually a fiction. Boynton's grade point average did not in fact entitle her to any degree honor whatsoever; but shortly before the ceremony, she had told Professor Davis in mock earnest that "my parents are here, so I’d really appreciate it if you could just mumble some Latin after my name".
She studied Latin for five years in high school—not so much out of a scholarly passion for classics but rather as an avoidance of science classes, the scheduling of which invariably conflicted with Latin. During her undergraduate and graduate years, her teachers included Cleanth Brooks, Harold Bloom, Richard B. Sewell, Maynard Mack, Maurice Sendak, Richard Gilman, Rocco Landesman, David Milch, Stanley Kauffmann, and William Arrowsmith. In an autobiographical talk given at Yale in 2002, "The Curious Misuse of a Yale Education", Boynton refers to her book Grunt (an illuminated book and recording of plainchant in Latin and Pig Latin) as "the culmination of a lifetime spent joyfully squandering an expensive education on producing works of no apparent significance".
Boynton intended to become a theater director. For graduate studies in drama, she attended the University of California at Berkeley for one year, then transferred to the Yale School of Drama D.F.A. program, but she did not complete the program. With the birth of her first child in 1979, Boynton postponed indefinitely a career in the theater, judging the demands of that profession not easily compatible with raising a family. She has been slowly returning to directing work: in May 1995, she wrote and directed a benefit reading, On Stage—featuring Jill Clayburgh, Joe Pacheco, and Jane Curtin—for Sharon Stage in Connecticut; in November 2005, and again in November 2007 she presented songs from Philadelphia Chickens, Dog Train, and Blue Moo at the Kennedy Center's Millennium Stage; and in November 2006, she directed her son Keith in his own play, The Quotable Assassin, Off-Off-Broadway at Alternate Stages.
In 1978, Boynton married a fellow Yalie, the writer and Olympic athlete Jamie McEwan, bronze medalist in the 1972 Summer Olympics in the C-1 event. McEwan was also in the 1992 Olympic Games, placing fourth in doubles canoe; in 1991, Boynton and McEwan moved with their children to the Hautes-Pyrénées region of France for a year, so that McEwan and his doubles partner, Lecky Haller, could train with the French team. McEwan has been a member of several whitewater expeditions, to Mexico, Bhutan, British Columbia, and a National Geographic–sponsored descent of part of the Tsang-Po River (Brahmaputra) in Tibet, an ill-fated trip detailed in The Last River by Todd Balf, and in Courting the Diamond Sow by expedition leader Wickliffe W. Walker. Boynton has illustrated two of McEwan's five children's books. They have four children: Caitlin McEwan, an actress; Keith Boynton, a playwright; Devin McEwan, a whitewater racer and member of the 2001 U.S. Team; and Darcy Boynton, a student. All four children are singers as well, and each performed on the Philadelphia Chickens recording.