The New York Triboro Overground
The New York Triboro Overground is a regional express rail for the outer boroughs. The Overground would utilize the railbed of the existing New York Connecting Railroad, which carries limited freight traffic and connects Port Morris in the Bronx through Queens with Bay Ridge in Brooklyn. The Connecting Railroad has a four-track right-of-way over much of its length, and carries Amtrak trains over a portion of the right of way.
The Overground could be put into use relatively quickly, in phases, and starting with diesel self-propelled trains. By reviving this train line, we could connect virtually every subway line in the city except for those that run exclusively in Manhattan and provide an inter-borough alternative mobility system.
The Overground is inspired by the work that London did to prepare for the Olympics, where they pieced together under utilized freight lines and surface rights-of-way to create a loop around London and integrated them with the underground and bus system.
This is not the only answer to the mobility needs of the boroughs, but it would certainly provide alternate means of access between the boroughs and into Manhattan.