The entire point of PBKDF2 is that a sub-$1,000 GPU isn't helpful.
It's certainly straightforward to use PBKDF2 in a way that is resistant to common / leaked passwords: add a per-database salt, then you can't go through the table in advance. For each individual user you want to target, you have to start trying passwords.
But even if you don't, the whole point of a password manager is to allow the single master password/passphrase to be something complicated. The average breached password should not be relevant here, and a good password manager's UX should encourage/force you to use something more complicated.
1Password, for instance, requires that you provide a 25-character random string in addition to your passphrase; it's not enough to just have the passphrase. I believe they're both used as inputs to key derivation.