UA has by far the best schedule on SFO-EWR, and they fly a good number of widebodies, many of which do (or will) have Premium Economy -- which normally isn't sold domestically. I'm not sure how UA allocates those seats, whether they're considered E+ or reserved for elites. But to Brooklyn that's a drag.
DL I think is all 757, which isn't particularly great in economy. (FWIW, UA/DL/AA/B6 are all flat beds in business/first class). But it has slightly more frequency than AA, and will operationally be more reliable. B6 kind of stinks operationally as well. No lounge option on B6. DL probably has the best membership lounge option on this route, at least on the NYC side (SFO is probably decent too). But if you're in paid business class, AA's Flagship Lounge at JFK is tops (but SFO isn't anything special). B6 will have the best base economy product (including free wifi) but they won't help you out on international.
I think this is a tough call because there are so many pluses and minuses of all the options...