I'm traveling from New Delhi to New York, and have Boston as a 2.5 hour layover. In the DS-160 form for B1/B2 Visa, I've filled New York as my entry to the US. Will this be problematic for my Visa approval?
If your Visa was approved, it is for the USA, not for a specific port of entry.
It doesn't matter which airport you enter on (or which sea port or street crossing), as long as your activities are within the limits of the visa.