The comparison between Authy and Clef is a difficult one to make on paper. While I haven't dug into Authy's security architecture as deep as I have with Clef, I'd imagine that technically the two solutions are very similar. Authy doesn't go into any detail about their security architecture on their website - which is one notable difference between them and Clef - but if they are following industry standards then both apps should be similarly secure.
With the technology similar, the big differentiator for me is market adoption (or likelihood of adoption). Passwords are used universally - if you've ever touched the internet, you almost certainly have a password. Replacing passwords, which both Clef and Authy intend to do, is a large task. Unfortunately it's also a winner-takes-all game. Most people don't really care that their passwords are insecure. Authy & Clef alone make it pretty easy to make the switch, but that only works if every site with two-factor authentication uses the same provider. Normal people aren't going to juggle multiple 2FA apps - if they have to do that, they're probably just going to stick with passwords.
In my opinion, the winner in the authentication game needs to get two things right: an approachable UI, and developer adoption. Clef wins in the UI world, hands down - you don't have to copy numbers from your phone to your computer, you get the pretty Clef Wave, and the whole process just feels very approachable. Authy feels like an enterprise company (and I think mostly, they are); Clef feels like a consumer company, which lowers the stress factor of using their app.
Developer adoption is hard to weigh for either side, because no major players have adopted either solution. However, Authy requires developers to pay, while Clef is free. If I'm a devoloper - especially at a startup - I'm going with Clef for sure.