Either are fine, really. JFK maybe slightly quicker going into the city - not necessarily true on the way back out because of traffic. Newark rally isn't that much further out. I'd go for which ever flights are cheaper (I've pften flown into one airport and out of the other).
You can get Port Authority buses from JFk into Manhattan, but I have always gone for a yellow taxi, which I think is $40 flat rate + toll ($5)? takes about 40-1 hr mins into midtown Manhattan depending on traffic. Allow longer on the way back, especially if you are travelling in rush hour.