They're different. Flow is not a "superset" of JS in that it introduces new features, it only introduces new types of annotations. Remove all the annotations (literally delete them), and you have valid ES6.

Typescript has its own class system, public/private/protected, and its own compiler. This was a big negative while ES6 was still brand new and the TS compiler was catching up, but now it's pretty much a wash between the two.

A year ago, I would have said Flow, no question. Today, TS has really caught up and the tooling is better, no doubt. It depends on how complex your types are - Flow can express types TS can't, but TS has an incredible ecosystem and far fewer bugs. In the end, it's all about reducing bugs in your own application, and TS seems to do that better in the end despite its limitations.