It appears there is one more. You want to head south to the Subway station. You can actually get in without removing any of the guards. The entrance is on the west side. Just drop down on the far side of the glass and hop the barrier to get inside. Go down the stairs and do a double takedown on the guards talking about reading. Go down those stairs and at the bottom, take a right and continue down more stairs. This should open into the actual subway area. Head to the back left and you'll see a vent that you can remove. You actually want to grapple up onto the train nearby. Walk along the trains, and you'll eventually have to slide under some pipes, hurdle over others and then break through (with a simple attack) some boards blocking an archway. You should hear a couple of guys talking about Solomon Grundy. Hop over to the next train and crouch under the pipes.
Turn right and drop down behind the group looking at the painting of Solomon Grundy. Try and take the left two in a double takedown and then you should only be left with one enemy. Dispose of him and turn left. There will be a shuttered door. Open it and slide under. You'll come to a stalker section. While you could try and climb up past the guards to do your thing, I find it easier to just hop into the grates. Get in the grate and follow it around to the far side. Eventually someone will come up from the tracks and walk behind some boxes, blocking view from everyone else. Wait for him to get behind the boxes, hop out of hiding and do a silent takedown. From here, it's just a matter of letting the guards come and investigate which will generally isolate them from the rest. They come in groups of two usually so you just need to wait for them to separate, take one down and hop back into the grate. Rinse and repeat.
Once done with that, head over and destroy the last jammer (on the far side of the train car). Once you are done with that, you can simply return the way you came. Just watch for enemies that you may have left hanging around outside. Once you get outside, if you use your grapnel, you'll probably climb right back up to the museum.
