My parents live 3 miles farther away from Manhattan's Penn Station than I do from Boston's South Station, so comparing commuter rail service from each home is a reasonable endeavor. Of course, New York is a much larger city, so suburbs there are more densely populated 20 miles out than they are here. So, I expect that trains run more frequently on Long Island, especially off peak (33% more into the city between 9 am and 5 pm). And, that stations are more convenient to more people on Long Island than they are here (by the time I drive the 6 miles south to get to the Framingham commuter rail station, I could be close to one-third of the way into Boston if I headed east instead.)
However, I do expect it to take a shorter amount of time to get from Framingham to Boston by rail than it would to travel the longer distance between my parents' home and New York City, especially since they need more stations to serve a more densely populated area. Yet it's just a 40-minute trip on Long Island, while most trains on the Framingham line are slated at just under an hour (56 minutes).
In other words: It usually takes about 50% longer to travel a shorter distance by commuter rail in Boston's western suburbs than on Long Island.