The Fung Wah and the Bolt are really cheap buses. For Bolt, I believe, the earlier you book, the better.
There's also the question of where your friend is going, both in Boston and in NY.
If she's (I'm assuming she's a she) going to midtown Manhattan, I'd go with the train, as it gets you to 34th Street and 7th Avenue (Penn Station), or the Greyhound/Peter Pan bus which goes to 42nd Street and 8th Avenue (Grand Central Station). They both leave from Boston's South Station and the train also departs from Back Bay Station in Boston and a Route 128 stop in the Dedham area which is outside the city of Boston.
The Fung Wah and Bolt buses leave from our Chinatown (Beach Street area) and go to their Chinatown (Lower Manhattan near Canal Street).
This is not to say that further transportation could not be obtained in either city. Both cities have excellent public transportation systems (both bus and subway/trolley) plus of course there are cabs. But there are some differences in terms of departure/arrival locations so they might need to be considered. By the way, if your friend is going to Queens, it might turn out to be best to fly.
I've taken the Amtrak Acela many times, and I love it. I will never take the regular Amtrak again unless I'm going to a stop that the Acela doesn't service. Acela is pricier but faster and a lot more comfortable. It's a few hundred each way, though. As for buses, they can be pretty good. It's been a long time since I took a bus so can't comment much on amenities.
A flight is 1 hour but you have checkin and baggage claim, plus you land in Queens so if you are going to Manhattan you've also bought yourself an hour or so of ground transport to get to Manhattan. The Acela is about 3, 3 1/2 hours. Regular Amtrak and buses both take around 5 hours.