Both are intended for distinct purposes. As a result, you may select them based on how you access your emails. If you use your email on several platforms, such as PCs and cell phones, IMAP is a better alternative. You won't lose your emails if you use IMAP since the originals are preserved on your server.
On the other hand, if you use your email on a specialized device, such as your workplace computer, you can use POP3. POP3 allows you to view your emails even when you are not connected to the internet. Unless you configure it on a server, your email is kept locally on your device.