I would say it would depend on the type of puffer, although i should also say, adding any fish in with puffers is a risk, since a puffer can turn on their tankmates...
Now as for the CAE, i did once have one with my palembang and it started to suck the slime coat off the puffer and never really ate any algae... so in all honesty, depending on the reason your getting a CAE, i would probably avoid one if possible...