CO doesn't consider EWR part of NYC, fare wise. They are playing to the corporations and pax who are NJ based, and are willing to pay more to fly out of EWR. Also there is NO COMPETITION what so ever for the non stops to the coast from EWR. VX tried to get in, unsuccessfully.
The lowest transcon fare from EWR usually $30 - $100 or more than the cheapest non stop transcon fare from JFK. If you are shopping for the cheapest coach fare, JFK will always be cheaper, because of the competition. VX, AA, DL and until recently, UA
However CO is seriously missing on on premium pax, who fly on contract/employer dime (NYC based), that allows business class 5 hours or >
From EWR
The domestic first (2 cabin) is usually $1500
Compared with JFK
Premium Business (3 cabin or DL Business Elite) is usually $2500 [ $1K more]
First Class (3 cabin) is usually $5600 [ though the studios pay much less to shuttle talent]
There is a reason why UA can make money having the plane 2/3's premium passengers. CO under Larry would never do that in a million years. I hope Jeff keeps it.