Avoid the 747 and you're fine. 777 best for economy as mentioned.
I actually prefer Newark - I'm based in NY for 6 months and doing a lot of back and forth. The taxi ride from JFK is endless, but the flat fare is good value.
Newark to NY comes in around $80 with tolls and tip but if you're staying downtown (Tribeca, Soho, Village) it's much quicker. Outbound even more so, have done in 15 mins. Take the train to Penn Station if you're on a budget.