Smith-9 Sts is the highest elevated point in the Subway system (80 or so odd feet above street level). You have a nice view of lower Manhattan from there. 191 St on the 1 is IIRC the deepest station in the system (there are runners up that is about 100 ft below street level i.e. Roosevelt Island on the F) and surprisingly, the subway becomes en El right after 191 St.
Be sure to check out the El's in the Bronx (1, 2, 4, 5, and 6 trains). Pelham Parkway has incandescent lighting on platforms (as regular lighting. no flourescents), the peaceful Sea Beach El (N train) in Brooklyn is something worth traversing through (as well as the other Brooklyn El's), and the R143's on the L and sometimes the M lines. The A train going to the Rockaways (there are two branches - Far Rockaway and Lefferts, so be sure to take the one to Far Rockaway) is scenic without question. A nice sunny day would help. And the Rockaways have two branches as well (one is served by the shuttle during non-rush hours) so be sure to check them both.
DANGER - DO NOT GET OFF MOVING TRAIN