Boston is one of my favorite cities. Joel On Software is planning a programmer's conference for September, and describes the city:
Boston is absolutely beautiful in September. The weather is usually perfect. You can go kayaking on the Charles [River] or take the Duck Tour(*) if you're unambitious. Over 250,000 college students have just arrived, full of completely unjustifiable hope and optimism. The summer tourist crowd has mostly gone home so you can get into museums and historical sites. There are plenty of coffee shops that aren't NASDAQ-listed.
Unfortunately, last time I was in Boston, it was middle of July and weather-dreadful. With daughter in tow, we endured umbrella-less downpours resulting from a passing tropical storm. Yuck!
(*) Duck Tours uses my photo of Newbury Street on their Web site's interactive tour.