Here is some info i found about the topic, hope it could help
In general, a master of engineering degree is oriented more towards professional development of practicing engineers. There is little or no research requirement and as a result there is a reduced expectation of focus in the program. Entry into these programs is generally less competitive, but they are considered poor preparation for PhD study. The expectation is that students will be entering/returning to the workforce following completion. Many engineers use these degrees to "top up" there skills as they climb the corporate ladder.
The masters of science degree is ... a typical MS degree. There is usually a thesis requirement and stricter admissions standards. While in engineering advancement to the PhD is not assumed, it is certainly easier from this position.
In general employers will care about the difference only when the MS thesis corresponds to a particular need at the company. Otherwise they tend to rank them equivalently. Universities do not, and will generally look less favorably on the MEng.
The advantage of the MEng is that it is easier to get into, and easier to complete, at the cost of a less focused education. The advantage of the MS is that you develop superior skills in your specialty and are more able to continue to the PhD.
All of these are subject to argument because every school does things differently - there are several schools (I am told) where the cases are reversed and the MEng is the research degree.