Anywhere close to a Red Line stop is good. Two of the densest areas are Kendall Square in Cambridge and the Downtown / South Station / Chinatown area. If you're close to either of those, you'll have easy access to events, coworking spaces, and other startups.
Personally, I love Somerville, around the Davis Square area. It's quick to get anywhere along the red line still, but the rent is cheaper and there's an arts / maker scene in the area that gives it a ton of culture. There are some standout startups around here too, including Better Lesson, The Echo Nest, and Pill Pack.
Please ask in additional questions you have as a comment to this, and I'll edit to improve my answer. I run Boston Startups Guide and have been here for around 8 years now.