Why is it dubious? Seems like every we should be moving to electrify as many rail operations are possible.
They are electrifying one line, for which there is no real imperative for that electrification (such as the tunnels around New York City's major stations), that only operates 90 trains a day? Or, to put it more accurately, for only... uh, 40,000 riders a day? You don't need electrification for this line.
The Northeast Corridor, with its 2% grades around the North, East, and (soon, with Portal's replacement) Hackensack rivers, its hundreds of trains per day (particularly, once again, around New York), and its 10-12 car multi-level trains being hauled at 100 mph (soon to be 125) require the 7000+ hp provided by electric locomotives.
Furthermore, the only line that serves Penn Station that was NOT electrified early in its life was the CNJ Long Branch. Given the complexity of switching engines at Woodbridge, its electrification had nothing to do with Green. It had to do with saving a lot of money and time, consolidating operations.
And ALL of this electrification exists for one reason, and one reason only, and that is the underground nature of the entire railroad infrastructure around New York City.
Electrification for electrifications sake is... essentially silly. BNSF's rambling on and on about electrifying the transcon makes a lot of sense. BNSF is owned by Berkshire Hathaway, which owns a LOT of coal mines. Coal is a very effective method of producing electricity with which to power... uh, BNSF trains running on the transcon. The money it would save them in both engines (electrics are more powerful), and fuel, is incalculable.