In the past, you could drive all the way out to an overlook very near Funnel. Now there is a fence delineating the boundary of the Wilderness Study Area (no mechanized traffic), which means a bit more of a hike is required to get to the river.
From the railroad bridge, take the Kokopeli to the cutoff that leads to Little Hole. Follow that in, and instead of turning in to Little Hole (now fenced there as well, with a pedestrian gate for foot travel in), go on out another mile or so, to the next major cutoff. There will be signage there (for what is called Hades Overlook), and there also should be another pedestrian gate. Park and hike in on the two-track, until you get to the very end of the "road". You will be on the upper level somewhere in the vicinity of Staircase. Way downstream, from that location you can actually see Skull.
From that point, you may be able to carefully work your way downstream farther and low enough to actually see Funnel and shoot your pictures.
Hope this helps.