Without a doubt, MIT CDO.
My understanding is that Stanford MS&E is not geared towards prepping you for a Ph.D. There are many things written about it on the internet, but basically its a flexible program with lots of course options. But its not a research degree. Same with Columbia MS&E. Both great programs, but they seem designed to send students into the workforce.
If you're serious about a Ph.D., then you absolutely want to build up a research profile. CDO is a thesis based program, and so when you get ready to apply for Ph.D. programs, you'll have serious research under your belt and MIT profs that can vouch for your potential as a researcher. That will do you more good than any set of courses or whatever GPA you get at Stanford MS&E, in my opinion.
Huge congratulations on all the offers though!