As someone who worked in the hotel industry for a few years, I gave out some of the best deals to people calling our hotel directly. The major websites such as Orbitz and Expedia charged 15% more on average than the general hotel rack rates. Rack rates at the rock bottom profit price that hotels charge. The allotments given by a certain hotel to the online travel websites are the rooms they plan to sell outside of the general hotel reservations system and are given to theses websites at a rack rate, then the websites up the price for these rooms.
To negotiate the prices, simply call the hotel. Ask for a reservations agent or possibly the reservations manager and simply tell them you have the rates of the major websites and would like to see if they have a lower price available. Explain to the hotel agent that you have been looking at the less expensive prices of some hotels in their area and some of their main competitors. You can expect to see some discounts of over 30-50% if you ask enough times about certain special VIP or Repeat Guest discounts.