Depending on when in September, it can be very summer-like in early Sept -- downright hot and humid, and late Sept can be very cool and rainy (sometimes temps can be in 40's), but usually in 60's and very lovely -- warm and sunny during the days and crisp and cool in evenings. Plan on some layers and a good raincoat. Sweater or light jacket might be necessary on deck in evening. Shorts if it's early in month, but if later then don't bother -- light pants or jeans will be fine.
As for foliage, peak in Boston area is usually around Columbus Day weekend, but earlier as you go north -- mid Sept in northern Maine if nights have been cold.
Like Mark Twain said about the weather in New England, "If you don't like it, just wait a minute." It is not unusual for the temp to drop 30º in 10 minutes, especially in the Fall!