The description of these two degrees is going to be different depending on the University. I took the Masters of Engineering option which was 30 credits instead of the 24 credits required in the MS program. The MS was more theoretical and was a good background for continuing onto a PhD program. The M.Eng. had 9 credits of professional breadth that was used for non-engineering courses such as business, economics, contracts, etc. I also liked the fact that the M.Eng. had a design project instead of a thesis which I wasn't interested in doing. One problem I had was when I completed 24 credits, I realized that I would have been done if I had taken the other program. It just made it a little more difficult to finish the last 6 credits.
I don't think there is any difference in the prestige, at least none that I have noticed personally. If I had it to do again I would probably take the shorter program since the course work would have been pretty much the same, except the professional breadth that wasn't that useful for me.
You should continue to ask around however, to get a better perspective on what you want to do and where you would like to work.
Good Luck,
-Mike