Are you hosting a server or just playing on one? For just playing, you should be just fine with it. Minecraft can eat resources, but I have a friend who run's on less than that and still runs smoothly.
CPU wise, yes the i5 4690k is a better CPU. It will be more expensive but with overclocking, can have a higher clock. If you don't mind spending more, then sure you can grab the 4690k, but you'll be just fine with the 4460. Since many games rely more on the gpu than cpu for performance and fps, of the two build options you listed, I would still go with the 4460 with the R9 290. If you got the R9 and 4690k, hey more power to ya.