I've flown to and from both JFK and EWR several times this year (from SFO). I've used the Airtrain/subway method (JFK), the airport bus method (either airport), and the NJ transit method (EWR). It's ALL good.

I base the decision whether to fly to JFK or EWR primarily on the airfare, because often there is a substantial difference. (Again, this is from SFO. I don't know where your sister is flying from.)