You don't mention the fact that AA business class would be much more expensive than JetBlue or UA in E+. So assuming cost is a non-factor...

Ordinarily I'd suggest checking out AA in business, but having an infant along certainly changes things. It would be a much longer trip, with two flights rather than one doubling the chances of weather/mechanical delays/cancellations. So, yeah, I'd suggest one of the non-stop options. And between the two I'd suggest JetBlue for the greater 38" legroom if you pay a bit more. Plus, even given that you're a 1K, UA is so lousy these days if there are delays or cancellations that JetBlue is probably the more reliable bet.

Also, JFK can get congested and delay-prone, especially afternoon flights.

Back to AA business for SFO-JFK, FWIW. Most of the flights are three-cabin 762s, which makes the J seats somewhat better than UA/AA domestic F in terms of legroom but not as roomy or good as international J. The one 763 per day (a two-cabin) is better, but still not quite international J in terms of service and (I believe, but am not certain) legroom. So both the 762 and 763 are definitely a more comfortable ride than in economy or even in regular domestic F, but not quite international J.