Cape Air won approval to start flights from Boston Harbor to New York City, at East 23rd St. in Manhattan. This is a one year pilot program for four flights a day.
Currently Amtrak is desirable for its downtown-to-downtown service, making up for slow train speeds by avoiding commutes for passengers looking to travel between city centers. This service offers to cut out the airport transit while retaining the speed of flying, though of course is subject to weather more than train travel. The major limitation, however, is frequency.