A couple of things to note:

1) is who is actually causing the congestion in NYC - its my understanding that the bulk of the congestion is caused by non-NYC residents

2) a large unaddressed component is parking - the large amount of free parking available, especially to non-residents, creates a distorting subsidy in favor of commuting in many areas.

If you want to read a great book on the broader subject, check out Traffic by Tom Vanderbilt http://tomvanderbilt.com/books/traffic/