Can you give more info, such as country and institutions you are specifically considering?
In the UK I don't think there is any great difference in MChem and MSci - one is not inherently better than the other. Differences the courses are more dependent on the institution than the label the qualification is given. Future employers will be more interested in the institution than the label as well. I would guess that MSci provides more opportunity to take specialist courses in biological and physical areas, whereas MChem is more directly chemical throughout.
Example: The Oxford MChem vs the Cambridge MSci in chemistry
Oxfords MChem is very much focused on chemistry from the outset, whereas the Cambridge course is broad, allowing you to pick modules from a variety of different scientific areas and specialise at a later stage (I don't think you can completely specialise in chemistry until third year). MChem graduates from Oxford and MSci graduates from Cambridge are both looked on equally favourably by employers, and both programs produce excellent chemists.