Ponyville, Canterlot or any other town/cities that is pony based just doesn't fit well within a humanized story, so what would you call them instead?

Depends on how the world is set. Is it still set in Equestria, magic and monsters in all? Or is it in a somewhat different universe? In either case one could use normal city names or make some of their own depending on the universal setting.

Canterlot - Camelot, Celestium

Ponyville - give it any name that seems to fit, maybe use a town name from a game or book that you like. Beregost, Rivan, or a complex name that is hard to pronounce like Worchiserville

The possibilities are endless

Baltimare, New Mare City, Chigacolt

Rumsville, Canterbury, Manhatten, Sauden Arania.

Cloudsdale... That'd be a toughie... If your humans had wings and horns similar to ponies, would the cloud city still exist?

I called Ponyville St. Charles in my humanized fic--though Ponyville's a justified nickname a lot of the locals use, due to it being the origin of the Pony Express.

As for the rest, I just use traditional names. IE: Camelot, Manhattan, ect/

I'll stick to some of the original names if I'm writing in a fantasy setting. For anything else, I'll probably change the name so it doesn't always contain a horsey pun.

Because rehumanizing horse-puns is surprisingly difficult, I would do one of the following: stick with the original name and give a good in-universe reason why it earned that name; give it another, unrelated name, but have everyone refer to it by the original name for some in-universe reason (like Ponyville being named The Town of Lord Saint Deboutant VI, but everyone calls it Ponyville for its horse breeding lineage and it's easier to say); go with a name that mirrors either the first or the last part of the original, but is flexible with the rest (e.g. Canterlot being Canterville, Ponyville being Peoplesburg, Appaloosa being Appalachia, etc).

Just remember not to hurt yourself too hard on the names. They're just names.

I kept all the same name in my stories... but there is an actual connection to ponies for my humanized characters. Either go with the parodied name (Canterlot) or just any name you want.

For me, I tend to keep things simple: If a town doesn't already have a human counterpartt, try to make towns with historical meaning. And if the characters have pegasi and unicorn features, then names like Cloudsdale should be acceptable, right?

Look at my chronivle and you see a few new towns and regions