The Secret Service office in Boston is a 2 mile drive from MIT. Once you decide to bring in the police, it makes sense that they'll contact specialist law enforcement that focus on computer crimes, especially since the Secret Service is so close.
My guess is it wasn't so much the Secret Service getting involved, but this DHS agency mandated by the USA PATRIOT act [3] made themselves available to major local organizations. Wouldn't be surprised if ECTF spent its first couple of years just meeting individual orgs one at a time for meets/greets.
"Have a computer crime that isn't just your usual Craigslist scam? Give Mike over at the Boston ECTF a call, and he can help you out."
[1] http://www.linkedin.com/pub/michael-pickett/15/722/660 [2] http://www.secretservice.gov/ectf_newengland.shtml [3] http://www.secretservice.gov/ectf.shtml