Boston as seen from Malone Park in Chelsea (aka Winnisimmeti) in November 2013
The folks over at Mental Floss have a great post on how the neighborhoods and towns around Boston got their names. Here's a couple of examples:
The area that now houses Charlestown was one of the first established European communities in the U.S. Originally known as Mishawum, Charlestown was “Full of stately timber and hospitable Indians” when first discovered. John Smith was among the men who first explored the area, and when he returned to England with a map, Prince Charles (later King Charles I) renamed the river after himself. The town adopted His Highness's name because of its proximity to the river.
The Massachusett tribe referred to this area as Winnisimmeti, or “Good spring nearby.” It was renamed Chelsea in the early 1700s after a neighborhood in London.