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It's not MTA, but the best public transit views can be had from the New Jersey Transit 128, 165 and 166 buses from the Port Authority along the top of the NJ Palisades on Boulevard East. The best views of the Midtown skyline, bar none. Metro North past Spuyten Duyvil on the Hudson line is also great for views the other way over the Hudson.
Otherwise, for subways, the 1 train over the 125th St viaduct has great views. The 2/5 in the Bronx is nice, too, especially along Bronx Park. The A to the Rockaways is an obvious choice once it reopens.
I like the Q52/53. Goes down Cross Bay Blvd and through Broad Channel. Also the Q76 [Francis Lewis Blvd], and Q35 [Flatbush Avenue, Newport Ave and over the Marine Pkwy bridge], although after Sandy I don't know how "scenic" these routes are.
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