Andrea: September is an excellent time to visit Massachusetts. You'll be too early for the foliage. But it is considered a shoulder season when prices go down and the weather is still good.
One of the things that might not be so obvious to someone from the PNW is that Massachusetts is a relatively small state in a small region. In fact, you could get in a car and hit all six states in New England in one day if you were motivated!
Many of the hotels in Central Boston are within walking distance to any of the major attractions. It is a very walkable City... from the modern restaurants and shopping of Copley Place and Newbury Street, to the older historic areas like Beacon Hill (with its cobblestone streets and gas lights) and the North End (with Quincy Market, Faneuil Hall, the Old North Church and Paul Revere house), not to mention all of the excellent restaurants and bakeries of Hanover Street (do go into Mike's Pastries and have a cannoli or a piece of ricotta pie!) The Boston Tea Party ship is a somewhat touristy ripoff. But the USS Constitution (Old Ironsides) and the Bunker Hill monument are worth seeing. There is a glut of lobster right now so prices are at their lowest in years and they will just be coming into season again in September (locals say months ending in "r" are the best for lobster). Try Legal Seafoods for excellent seafood and chowder.
All of the kids will be coming back to the ten or so colleges in Boston around that time. Everything gets really vibrant and energetic. Don't forget that Cambridge (with Harvard, founded in 1636, and MIT) is just across the river too.
Salem is a very easy drive from Boston. Just be careful of some of the witch attractions that can be really touristy. You can certainly see everything there is to see in Salem (House of Seven Gables, etc.) in a day. If you get an early start you might expand your drive to include Cape Ann, Gloucester, Marblehead, etc.
Not sure if it is on your radar, but Lexington and Concord are an easy drive from Boston (up Route 2) if you're interested in seeing some of the historic sites out there (including Walden Pond) too.
With traffic it is about a two hour drive from central Boston to Hyannis, the largest town on the Cape. (Don't forget that Plymouth Rock and Plymouth Plantation are on the way too). Some of the highways to the Cape are lined with cranberry bogs which will just about at the point of early harvest when you are there.
Falmouth and Woods Hole are lovely areas and places to get the one-hour ferry to Martha's Vineyard. But I much prefer Nantucket which is a two hour ferry ride from Hyannis (They also have a high speed ferry). Jetblue also flies from Boston to Nantucket and it is a quick flight. If you're into history the whaling museum of Nantucket is a must-see.
Massachusetts natives overwhelmingly summer in the beach towns of the central and lower Cape, mostly because it is an easy drive and summer traffic can back up. But do invest the extra time to explore the outer Cape. Everything from Wellfleet on up to Truro and Race Point and then, of course, Provincetown. Visit the Highland Light near Truro and you might see humpback whales just off the bluffs there.
Have a great time!