That's because Boston and NYC are both navigable without a car. Only one side of the SF-LA link can claim to be close to that ideal.
But the time and hassle of airport parking and security and delays might be able to keep a 3.5 hour train ride viable even in CA. That would require a train system that allowed passengers to step through a quick scanner with no line and onto the train without queueing or carefully organized boarding. Lots of train systems used to do that in the USA but the bureaucrats don't like passengers freely walking around platforms by heavy machinery or directing themselves or quick predictable security procedures. Acela has been abandoning efficient and established traditional practices to copy instead the airports. How long are they going to stand for a train system that isn't as awful as airport security and boarding?
Since politicians can't risk being blamed for trouble, we have no ability to control the bureaucrats and every high speed transportation system will inevitably get to be as bad as airports.
If rail could be built at the same costs as in France or Japan (or even, optimistically, Spain or Korea), to wit, $20-30MMM, you could justify it just for saving the cost of airport expansion. But at $80-120MMM it's lunacy to proceed.