Here is the simple -
You will spend $15 on toll ONLY via car/livery from EWR -that doesn't include charges for car/service.
Also, EWR weekend train service has gaps in service (either top half or bottom half of hour so it you miss the bulk of inbound service you may wait up to 35-40 minutes) vs. I anticipate it will take 40 minutes maximum from JFK.
As many others indicate
JFK is the ANSWER - very fast (via public transportation), economical and you end up precisely at Penn Station. Just verify you buy weekend SAVER ticket on LIRR vs. regular off-peak fare.