New York Magazine hired Nate Silver to create a ranking of New York neighborhoods based on quantitative analysis. He finds that Park Slope comes out on top.
In the model he developed, housing cost is the largest factor affecting livability followed by transit measured by commute time. It is difficult to disentangle these factors as people trade transportation access for housing costs. I think access to opportunities overall is a better measure than commuting, and he notes that small changes in other measures creates big results. The story also has a nifty livability calculator to test your own ideas.