First, you can mark kyou with ni, because it's a time expression (which makes it an adverb). But there's no reason to do that here, because in this sentence you're trying to say that as for
today, compared to other days, John is doing great. Kyou is the topic that grounds the sentence. So you want to mark it with wa.
Second, John can be marked with ga. He's the subject of the sentence.
Third, you don't necessarily need to mention John at all, because you're speaking right to him and presumably it's already established that you're talking about each other's health/attitude/whatever.
As a last bit of information, wa throws attention forward while ga throws attention backward. So for example,
ii <-- neutral sentence. John's good.
john wa ii <-- emphasis on ii. John is what? John is
good.
john ga ii <-- emphasis on john. Who is good?
John is good.
I'd like to reemphasize that a neutral sentence doesn't mention John at all.
Anyway, that's all I got. Good luck. Learn the kana