JFreeChart
- very sophisticated. you can do more stuff in it than in JavaFX.
- API is not easy to understand. You need to put a lot of effort in it to get your charts working like you want to.
- Official Dev Guide and Sample Code, which I'd recommend, are not free.
- Project seems to have stopped being developed (last changes are more than 2 years old)
JavaFX
- Good enough for most usecases.
- Well documented and easy to understand (and completely free)
- In active development (with Mailinglist and Jira).
- Officially supported and featured by Oracle.
Choose your destiny.