I'm a United 2P and do this route at least once a month. I rarely do it on United. The primary reason for this is price: the UA PS flight is considerably more expensive than B6 or VX most of the time.

All things being equal, I take the UA flight due to miles, but I never count on an upgrade even if I am using miles or certs to upgrade (which I always try to do). Any reasonable flight times are PACKED with 1Ps and 1Ks that will get priority before you do. I like the PS flight because while there isn't any TV (I can read anyway), there is still power for my laptop and as others have mentioned, that's a lot of miles I want credited to my account.

When UA prices itself out of competition, I tend to prefer VX vs B6. This is primarily because I'm not a huge guy (5'9") so the small difference in seats doesn't matter much for me. The in seat power us huge for me, and I like that I can actually get some decent food on the VX flight vs the B6 flight if I'm cramped on time. I also hate the B6 terminal at JFK - it's a dump. One word of advice on VX - get an aisle seat. The seats pitch pretty far back and if you are on a window, it's really difficult to get out of your seat because of the recline of the seats in front of you.