If you're going to be commuting into Manhattan you might want to take a look on the other side of the river. There are 3 train lines in Westchester and Putnam Counties that go direct to NYC. They have loads of trains and just added more to the schedules. No matter how you look at it, at any given time crossing the Hudson can be a nightmare.
If it's the Westchester prices that throw you off, it's really worth taking at least one look at Putnam County. You might be pleasantly surprised.