I will Prefer Kayako. I really like its features.

Kayako has better features but Zendesk seems to be used a lot more but that's just my opinion.

I've used most of them for various businesses and I prefer (not in any particular order):
Kayako - Very powerful
Freshdesk - Powerful and VERY user friendly
HelpScout - More like email but very powerful and feature rich.
Zendesk - No. There are better options (just my opinion).