I had this same question multiple times last cycle. Be sure to make sure that both the MSAR and school website data is for the same year. Sometimes one data set is more recent than the other.
I would recommend taking both into consideration, since MSAR gives a percentile range of data and school sites usually just give averages. When I was applying last year, a big part of gauging my competitiveness for my target schools was seeing if my GPA and MCAT fell within the 25th-75th percentiles listed on MSAR. However, I wouldn't recommend being too overly rigid in this regard for your entire application list. My GPA was 99th percentile but my MCAT was <10th percentile for the school I'll be attending this fall.