Hi! I'm in the same position as you! To help decide between the two, I am going through the various courses that are offered in each program to see which ones I am more interested in.
The MT program has a stronger research component to it, since you have to do an extensive research project, so that is important to take into consideration!
The MA CSE program does have unique benefits to it, including access to the lab school and the program's focus on only primary/junior teaching.