I would go through ORD on the 789 and take my chances on the seat type. I prefer the Polaris seat over the old CO 2-2-2 seats quite a bit, but avoiding EWR and shortening the trip by an hour would be more important to me.

ETA ... not sure when you are flying, but schedule and equipment swaps happen frequently, so if it’s more than a few weeks away I would anticipate something changing between booking and the time you travel.