3CCD or monochrome with Bayer filter?
Generally Bayer mask (also known as CFA = color filter array) imagers are the most popular. 

3Chip cameras cost considerably more - you are not only paying for 3x as many chips but the alignment in manufacturing is expensive and the range of cameras is much more limited. The largest are HD (1920x1080) although a lot of cameras actually have much smaller chips and rely on a deliberate half-pixel misalignment to interpolate each colour into a higher resolution - as with a CFA. Since most are aimed at the TV market they are usually video output (so you need a grabber card) and are a fixed TV frame rate

There are potentially aliasing issues with CFA cameras if you have a very small point image which may hit only one of the colour cells, this can be fixed with an anti-alliasing filter which blurs the image slightly, or by software.

One area in which 3chip wins is in low light where you need high colour quality. A 3chip camera detects essentially all the light in the scene in each colour. A CFA will detect only 25% of the Red and Blue and 50% of the green since the other photons are blocked by filters.