Haven't tried this desktop app yet, but WhatsApp web already shows notifications, at least using Chrome.
If you don't care about the notifications, you could use Fluid to make a standalone app which wraps the website.
Why is it better that Node Web Kit?
Does it worth it ? (not a regular whatsapp-web user).
[1] https://github.com/Aluxian/WhatsApp-Desktop/blob/master/src/...