UA has the most nonstops from SFO-NYC (particularly if you throw in CO flights to EWR) but AA, DL, B6 and VS also have decent schedules on this route. So any of them are viable - it just depends on your needs.

If you are flying on your own dime or need to keep costs low, I would not recommend UA as you will usually find cheaper fares on the others.

The 50k benefits are roughly equivalent on UA, AA and DL, which include 100% RDM bonus, priority checkin and security lines, partner lounge access when flying internationally, free checked baggage allowance and priority for upgrades.

If you are looking to upgrade you probably need to collect and compare data from UA AA and DL flyers on these routes. UA/CO offer unlimited domestic upgrades but they may be tough to get given the number of high level elites at SFO. However UA also offers E+ seating which is a nice perk on transcons (though I rarely had difficulty booking exit rows as an AA elite).

If you are looking to use miles I find AA generally the easiest to redeem, with UA not far behind. DL has a well deserved reputation as the worst. B6 and VS are generally acknowledged to be less rewarding particularly if you are seeking the holy grail of international business class saver award tickets.