This is one of my pet peeves with NYC airports (EWR excepted).
Like Boston, the NYC bus/ subway connection appears to be designed to be inconvenient.
At Logan, you must board a bus ( different busses for different terminals ;-) and then wait for the interminably slow Blue line train which goes to the wrong parts of town. Connections, etc, and one hour transpires for a simple three-mile journey from Logan to the true center of Boston (Copley). I have heard that the system is designed to be slow because of taxi drivers' concerns about fare losses.
NYC has this problem, perhaps worse than Boston. Cities of this size should have a one-seat system to get arriving passengers into the center of town (in NYC probably both Midtown and Downtown) at a three dollar fare, maximum.