WhatsApp is more popular.
According to statistics that I could find, Skype has 300 million monthly active users (as of Oct 2017) and WhatsApp has 1.5 billion active users (as of Jan 2018). Even though these numbers are a year old, there is no way that Skype could reach WhatsApp in terms of popularity.
Skype is an app which is mainly popular for Audio and Video calls over the Internet(even though it supports chatting), while WhatsApp is popular for messaging(though it supports calls). So normal people would generally prefer texting over calling many times. WhatsApp launched as a free messaging app over the Internet when telecom carriers used to charge for SMS. So it became a mobile to mobile thing while Skype was used mainly on computers to make video calls.
When it comes to business chats and meetings, people still largely depend on Skype, though they have friendly whatsApp groups these days.
https://expandedramblings.com/index.php/how-many-people-use-chat-apps/
