If you don't mind a bit of grungy asthetics, the areas near the JMZ trains just on the other side of Manhattan in Williamsburg and the Bed Stuy/Bushwick border have a relatively fast commute - much faster than far more expensive neighborhoods in Brooklyn.

For example, it's like 10m from Marcy Ave to Essex St. in the LES. The J goes downtown in the Wall St. area while the M takes much of the same path as the F along 6th Ave, and both of those trains follow the same lines up until Myrtle-Broadway. In fact, it's literally two stops from Essex St. during rush hour as the J runs express (sometimes it sees itself as a Z).