I used Lastminutetravel to find "cheaper" hotels in Manhatten--then I called the hotel. The site had a rate of $139, but the hotel had a manager's special of $129. The hotel was about a block from Penn Station, so not the best neighborhood, but not bad for $129!

The moral is, take the time to call the location. You might be able to bypass the site altogether, feel more confident in your reservation and maybe get a better deal!