Prices for hotels in NYC have been pretty much sky high all summer. We stayed at the Milford a few weeks ago, the cheapest we could find. Small, but clean and cheaper than most of the others but not really cheap. Was just in NYC yesterday(Tuesday) with my daughter and could not find a hotel in the city for less than $400. We opted to leave the city after her appointments.
What I would recommend is looking into hotels in Secaucas, NJ. We have stayed at the Hilton Garden Inn and La Quinta many times. It is a 10-15 minute ride to the city by car. The train station is not far away and we have got a bus or shuttle to the station from our hotel. It saves alot of money staying in Secaucas. La Quinta also offers complimentary breakfast, whcih is nice.
Once in awhile it is nice to stay right in the city!