(Not from NYC, but)
I found it hard to navigate due to not being able to see far enough ahead and not knowing which transfer to take to head in the direction I want (is it Ⓡ Forest Hills-71 Av or Ⓡ Bay Ridge-95 St to head left/East at Lexington Av/59 St?). So, uh, I planned ahead using the subway diagram [1] (is that cheating?). I got:
127 stations, 69.92 miles, 5:02, 4 boroughs, $3.00
Station Transfer
------- --------
⑥ Pelham Bay Park
Lexington Av/59 St -> Ⓡ Forest Hills-71 Av
Forest Hills-71 Av -> Ⓔ Jamaica Center-Parsons
Sutphin Blvd -> Ⓩ Broad St
Broadway Junction -> Ⓐ Inwood 207 St
Jay St -> Ⓕ Coney Island Stillwell Av
W 8 St-NY Aquarium -> Ⓠ 96 St
Times Sq -> ② Wakefield-241 St