We chose to take a Circle Line boat trip from Pier 83, down the Hudson, out to Statue of Liberty (but not stopping) and up the East River... I think it was called their 'Landmark Cruise'... it was a really good option.
Yes, it has been discussed several times... from our visit last June... I would thoroughly recommend walking the High Line, walking across Brooklyn Bridge and visiting the Lower East Side Tenement Museum among many others.