Schnit

I would look for something close to Hoboken or Newport PATH stations. They will be on the water right across from NYC. The PATH runs between every 5-30 minutes depending on the time of day, and runs all night. Only 2.75 per person each way.

I have never stayed at any of these personally, but looks like there is a W Hoboken and near Newport there is a Courtyard, Westin and RI.

I have stayed in multiple NYC hotels over the years and they are tiny. I couldnt imagine staying in one with kids unless we got multiple rooms. I travel with 4 kids, so if it were me, i would give the RI a serious look, but dont know your budget/needs.