The Esplanade is a beautiful place to walk or run and see the city. The green space runs along the Boston side of the Charles river from the Museum of Science to BU (& beyond). You'll be sure to see geese and beautiful trees, and might even see swans, jumping fish, and bunnies if you're lucky. Special note: the Owl's Nest (a.k.a. Goose Caboose) is our favorite beer garden-- stop and have a drink and a snack.
Cafes & Bakeries: Area Four Cafe (quick homemade pastries and my (Jessie) --hot take--favorite croissants here), Cicada Coffee Bar (favorite for lunch), Bloc Cafe (nice cafe in Union with lots of veg options) Seafood (Boston!!): Judy's Bay (izakaya, our favorite), Row34 (fancy), Alive & Kicking Lobster (takeout, lobster sandwiches) Other Dinner & Drinks: Blossom Bar (also great for dinner, cocktails are the best), MaHaniYom (Thai tapas, our favorite Thai in Boston), Spring Shabu Shabu (AYCE), Punjabi Dhaba (Indian a few blocks south of Union Square)
There is no shortage of fantastic museums in Boston, but these are our favorites: The Harvard Natural History Museum (widest range of taxidermy deer sizes this side of the Mississippi, and crazy intricate glass flowers), the Isabella Stewart Gardner Museum, and the Museum of Medical History and Innovation at Massachusetts General Hospital (and the nearby Ether Dome). All are close to the T or a short Uber away.
The Freedom Trail is a unique collection of museums, churches, meeting houses, burying grounds, parks, a ship, and historic markers that tell the story of the American Revolution and beyond. There is a self guided walking tour you can take anytime or you can purchase tickets for the guided tour that leaves from the visitor center at the Boston Commons.