Is it really just two days?

In that case I'd recommend parking in Manhattan. People tend to freak out about parking (and driving) in the city but in my opinion that's an overstated worry.

For two nights it seems like an easy call. Find a discounted or cheaper lot in the city relatively close to your destination. There are 24 hour tended lots all over, and the ones further from the subway and central business districts are often quite reasonable.

Parking and taking the train involves paying a fee for parking (usually) and then the train, lugging any baggage, and then getting from the NYC train station to your final destination. And if it's just two days you'll be lucky to save $20 or so for all that effort.

Parking in the city means you can often run by your hotel or destination and drop off bags (especially if there's a bell staff), and then drop off your car. It will save you probably two hours, lots of hassle, the trouble of trying to time it to hit a train schedule. Flip side is maybe a few dollars extra for the parking and about 6-9 dollars for the toll. And if it's rush hour perhaps the traffic is an issue, off hours that's not a concern.

There are many services like bestparking.com that will give you rates and some that will enable you to make a reservation in advance, so you don't have to look around for a lot.

That's my recommendation.