I think career numbers are less important because, well, first off I would not include anything about 2016 in assessing Goff. And with Stafford what he did as a rookie, in 2011, 2013, etc does not matter much to me either.
Compare the past 4 years. I looked it up last night and I believe the QB rating is 96.8 for Stafford and 94.1 for Goff. Difference being MS has been pretty consistent while Goff has trended down the past two years.
And yes, I agree you have to factor in the organizations they have played for. Grade a bit on a curve there and MS probably comes out further ahead.