Personally, I'd pick UA on this route just because you have the p.s. flights out of JFK (which are good for non-elites because the entire cabin is E+) supplemented by often cheaper options out of EWR. I find EWR-SFO not too bad for upgrades (paid premium traffic tend to fly p.s.), especially when it's served by 757s but as a Silver the chances are slim at best. I don't often pay for premium cabins on these flights so I usually end up going EWR-SFO.

My second choice would be DL due to their good C product on this route and I'd put AA in last although their FFP is pretty good.