The Ultimate New England Fall Ball
Day 1: Fly into Boston Logan & pick up rental car
Grab your car & get the heck outta dodge! Depending on where you fall on the leaf-peeping schedule and when your flight arrives, I think you should grab a bite to eat, maybe stroll around Harvard sipping my favorite sparkling lavender iced americano, and then head to Salem. You can explore a bit more of Boston on the back-end (or front-end of your trip if you arrive a little early for the leaves).
The drive from Boston to Salem is ~31 mins but it's scenic so there may be some wishes to pull over and take a picture.
Check in: Hawthorne Hotel (1 night). Schedule a ghost tour to learn about the Salem Witch Trials. You could easily do 2 nights here and explore The House of Seven Gables and learn about the pirate history of Salem.
Enjoy dinner at The Tavern!