You should be able to check your bags through to Malaysian, unless for some reason CO does not have an agreement with them. (No such luck on return, however.)
Assuming that is the case, I would agree with the 60 minute assessment. Assuming you fly into C, it could easily take you 10 minutes to get to the AirTrain, depending how far your gate is. Add 5 mins wait for the AirTrain, prob only 1 minute between stations, and then check-in and security, you will have chewed up 30 minutes already.