MtGox is an exchange: people trade Bitcoin for USD there. The value they report is what the exchange rate is on MtGox.
CoinDesk calculates its Bitcoin Price Index based on a number of factors, including MtGox's price, and the prices on other exchanges. This appears to be a much better indicator of the true market value than MtGox's exchange rate.
You might wonder, if the price difference is so large, why don't people buy on one and sell on the other to make a profit? People do, in something called arbitrage trading, but how close this will bring the markets depends on the overall costs of the transactions (fees, etc.). Since getting USD out of MtGox is not easy (or even possible?) at the moment, the gap can be quite large.