If all things are equal with technology in a sensor and they are the same sized sensor, then the one with the lower MP will be better with noise in high ISOs. The problem is that each sensor is different and with different technology and different ways of processing the photos.
For the most part, size of the sensor will make a bigger difference on the noise in high ISOs.
There are a number of cameras that can do great in high ISO with low noise. Some that are considered the best are the Nikon D3s, Nikon D700, Canon 1D Mark IV,and Canon 5D MarkII. Those cameras also need to have a large aperture lens attached. You'd be looking between $3500 and $6500 for one of those bodies and a large aperture zoom lens.
To a lesser extent, there are DSLR bodies that don't do as well as the previous ones mentioned do, but they do very good, for the price. The best low light DSLR for the least amount of money would be the Pentax K-x. You're still looking at over a $1000 for the camera and one large aperture lens.
If that's still too much then you can look at the compact cameras. The Canon G11 and the Canon S90. The difference between the first cameras I told you about and these are very large for noise in high ISOs. It's just what your requirements are, your budget, and how much you're willing to compromise.
Can people recommend good cameras for low-light photography?
I've heard elsewhere that for better low-light performance(less noise at higher ISOs), it is better to have fewer megapixels for the same size sensor because it means each pixel is getting more light. Is this true?
Are there any specs that are good indicators of low light/high ISO low noise performance?

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