Performance
While both lasers function exceptionally well in low-light conditions, the advantage of the green laser becomes evident in well-lit conditions. Red beams are often hard, if not impossible, to see in daylight, but green laser beams are relatively easy to see during the day.
Availability
There are more variations of red laser sights available than green. However, as the popularity of green laser sights increases, it is reasonable to expect greater numbers of green laser sights entering the marketplace.
Cost
Red laser sights generally cost less than half of their green counterparts, but if practicality and usability is your chief concern, then spending the extra money for a green laser makes sense.