Best photo ops in the system: curve at Smith-9th Sts on the F/G line, Coney Island-Stillwell Av on the D/F/N/Q lines, Whitlock Av on the 6 line, 161 St-Yankee Stadium on the 4 line (get a train and the stadium in one shot), Park Avenue tunnel portal on the Metro North Railroad (can't remember exactly what street).
The Brighton Line (B/Q lines in Brooklyn) is very scenic and some stations appear to be in a deep forest. Neck Road on the Q line is a very good example. The whole line from Prospect Park to Coney Island is a great line to railfan.
And of course, the 7 line is a railfan's dream.
Hope this helps.