Consider the cost and convenience factors, and decide for yourself. Call the hotel to find out how much they charge for parking. Let's say it's $25/day. Find out out much it's to park at EWR's long-term lot.
If you drive into NYC, you pay the bridge/tunnel once, for about $8. If you park in NJ, you have the fees for R/T transportation for 4 people. And you have to take luggage with you onto shuttle bus, a couple of trains (or another bus), and to the doors of the hotel, and the extra time, etc...
If you park at a NJTransit lot, really ask around security.