I think the main differences are in the type engines. From what I have seen, Flow can infer much more informations about a program, even on unannotated JavaScript. As a result, with the same amount of annotations, it seems to me that you can find more bugs using Flow than using TypeScript.

TypeScript recently added an allowJS mode which makes it much easier to convert JS to TS a file at a time and Typescript will infer what it can from the unannotated JS files. From what I hear it's not quite as much as Flow picks up, but it is getting better, especially because it's also doing double duty as the new JS IntelliSense language service (codename "Salsa") for VS Code and intended to eventually replace Visual Studio's IntelliSense language service for JS as well.

I find typescript pays off with the excellent intellisense and refactoring in editor support. They did a great job of having the language service and compiler use same core code base.