Having done both, I'd probably say the MCSE is harder.
I base this on the fact you've got to pass something like 7 exams (compared to 1 for CCNA). Also the material changes quite a bit for each subsequent OS release which means keeping your skills and certification updated is a lot of work. In comparison, whilst CCNA tests a wide area of Cisco networking concepts, these are fundamental concepts and thus the exam content changes very little over time.