Which puffer?

Depends on the species clown you go with.. Canthigaster species(toby, spotted, leopard) puffers don't get to large (5"ish) but could probably fit some smaller clowns in their mouths.

Some other puffer types are more aggressive, but the ones I mentioned are fairly peaceful, dog faced type are also pretty peaceful and can have tons of personality but are even larger. I would think maroon and tomato clowns would be ok as long as the puffers aren't adults and clowns juvies, but perculas and osellaris adult males might only be 2"ish

Keep in mind that with puffers, you will need to feed them an appropriate diet to keep teeth trimmed--or have plans to undertake marine dentistry. Most puffers are not piscivorous --they eat clams, mussels, shrimp, anything crunchy. This diet keeps their teeth short, otherwise, like rats, those teeth keep growing and can get to the point where the fish can't eat anything. The bigger concern would be nipping fins, and tobies are worse in that regard than dog face or burrfish.

I'm a huge fan of the burrfish and dog face puffers. Friendly, outgoing, curious...they're like little puppies. Tobies are cute, but they aren't as interactive with owners as the dogface and burrfish. Burrfish come in a few different color patterns, and unlike the pufferfish, most stay around 8-12 inches as adults.