I just rode it last week, and it actually took 3 hours, not 3.5.
Most of the NEC corridor from DC to NYC has a speed limit of 125mph; from NYC to New Haven, it's generally 70mph (!), from New Haven thence to about Kingston generally 90mph, and from there to Boston it's mostly 150mph. Given the density of the corridor, Amtrak should be trying for 150-220mph speed limits, but even 125mph is generally agreed upon to be the lowest end of HSR.
A surprisingly easy way to make the train go faster would be to redesign the switching sections before large stations to allow trains to go faster through them. You can probably cut around 10 minutes out of the entire length with an investment of less than $100 million just by doing that.