Here's my opinion on the two libraries.
Both are great options.
Puppeteer is a neat library, but it is limited to just Chrome. It also doesn't come with ready-to-go utils for third-party services like Sauce Labs or test reporters.
If you're looking at writing a simple web scraper, or have some form entry you want to automate for non-testing purposes, I'd say go with Puppeteer.
But if you're looking at writing test automation, WebdriverIO is going to give you a lot more functionality for not much more effort.
So choose the tool depending on the need you have :)