They may not be harder to clean per se, but they do take longer to clean. Glass is impervious to pretty much anything we homebrewers can throw at it, so, given sufficient time soaking with a good, strong oxyclean/pbw/whatever solution, there's nothing that won't come out. But you can't just give it a quick scrub with the soft side of your sponge and be done.
Carboys are also more of a pain to take gravity samples from – maybe not that much of a pain, but certainly harder than "sterilize spigot, open spigot, close spigot, rinse spigot."