Given the current state of the art, the noise in the blue channel is a combination of cascading effects that work together to make the blue "look" the worst. First, with the Bayer pattern setup, there are twice as many green pixels as red or blue ones in the matrix*. This immediately puts the blue and red at a spacial disadvantage as compared to the green channel and results in much more spectral noise for those two channels when the RGB triplets are reconstructed from adjacent sensor pixels. For example, a 10M pixel sensor is going to have 5M source green pixels, 2.5M red ones and 2.5M blue ones. Clearly, when you form that raw information into the final 10M RGB triplets, it's clear that there can be no better than 1/2 as much information for red or blue channel and this appears as a form of noise in the final image.
The next effect has to do with the spectral sensitivities of the sensor system through the Red, Green and Blue filters. As a system, modern CMOS sensors are about 50% more sensitive to the Green and Red areas of the spectrum than they are to the blue areas. For example, for this CMOS sensor from Cypress, we can see on Page 3 that the relative sensitivities are about Red (75%), Green (80%), Blue (50%) when you index the curves at the right wavelengths for each color. This lack of sensitivity combined with a fixed level of sensor and sampling noise for all pixels across the sensors put blue at a significant signal to noise ratio disadvantage as compared to the other two colors.
Netting this out, this means that color CMOS sensors are doing the best at reproducing Green, followed second by Red, and finally by Blue which is the worst of three from an overall noise perspective.
Looking toward the future, note that these limitations with the blue channel are really mostly a matter of a cost/performance optimization. That is, there is nothing inherent to physics that requires blue performance to be worse, only that it would be MUCH MUCH more expensive given current device constructions to improve the blue channel by a noticeable margin. Also, given that the human eye is not very sensitive on the blue/yellow color axis the solutions are already a very well optimized solution. In fact, I'm sure most camera makers would prefer total cost to drop first before paying the same or more just to improve blue channel noise performance.
*Bayer chose to setup the matrix this way because the human visual system gets the majority of it's luminance signal (ie: brightness information) from the green part of the color spectrum. That is, the rods in the eyes are most sensitive to green light making the green part of the spectrum the most important visually.