I think my favorite hotel I've ever stayed at is The Roxy in TriBeCa. An amazing staff, the nicest I've ever encountered in a NYC hotel, with great restaurants and night life and 24 hour room service. Plus I love the location, and it's an easy train ride on the A or C to Time Square. I've never not stayed there at a discounted price.
If I ever need a hotel in NYC and don't use rewards points or union discount, I almost always use Hotwire. I feel of all the discounted hotel sites, that one always has the best rates for NYC. Like I love the Hotel Tonight app, and that is great for Vegas, or Anywhere but NYC.
I know a lot of people don't like Hotwire because you don't know what hotel you will get until you already purchase it, but I have found that if I filter only 4 and 5 star hotels and only pick Boutique Hotels in neighborhoods I'd want to stay, I've always been very satisfied. $100 a night on average (plus the fees) for rooms that would be $500 give or take directly from the Hotels website. Through Hotwire, I've gotten The Ganesvoort in the MP district, The Roxy, The Roger, The James, and Crosby Street.
But, I also don't have a problem hopping from hotel night to night to get the best deals on my lodging. I also will wait to the last minute to book a stay for the best deal. I know a lot of people prefer to plan everything in advance.... But I've actually gone to NYC and not even booked my room until already in the city, knowing I'll get a good deal last minute and watching as prices kept falling.