I did go down that list. See the second section of http://www.paulgraham.com/siliconvalley.html .
So, the Boston area has had more time with its universities, rich people, and population base to develop. Yet Silicon Valley developed faster and came to be the bigger innovation center. Again, I suggest there's something else at work besides the presence of top-flight universities, rich people, and time.
What is interesting is that New England was a major force in innovation during the second half of the 19th century, helping to drive the industrialization of the US. So, whatever factor that brought innovation to the Bay Area had to have been strong enough to unseat the existing innovation centers.