FWIW, this week's Washington City Paper cover article is about ways to travel between Washington and New York using public transit but without using Amtrak (or Greyhound). The author of the article actually took that trip one day in April.
Here's the link to the story:
"The Third Rail: One Man's Quest to Take the Train to New York Without Ever Boarding Amtrak"
(Incidentally, the cover of the print copy of the 5/9 edition of the Washington City Paper features a picture of a SEPTA Regional Rail train.)