What are some good manga sites that allow me to buy and read manga on my iPad? I downloaded Kindle on my iPad but I can't seem to get any of the manga to read on it.
Also, if you bought the physical copy of a manga from Amazon, could you also read it through Kindle?
You have to buy digital versions separately.
Viz has an app, which is what I use for their stuff, but their manga is also available on comixology, and purchasing in one place doesn't cross over. It's just that I've bought so much via Viz directly already. You can also subscribe to Shonen Jump weekly if you like Shonen jump stuff. They currently run One Piece, Black Clover, Hunter X Hunter (when it comes out), World Trigger, Nisekoi, Bleach, Food Wars, and Toriko weekly and monthly installments of Blue Exorcist, Seraph of the End, Boruto, and whatever Yugioh is currently running, all the week (or week after) Japanese release. You can get a years subscription for 25 bucks regular price. They also have a separate Shonen Jump app just for that, but you can read it through the Viz app fine.
Comixology is the app that most comic companies use, including DC and Marvel and Image, but also Viz, Kodansha and others. They were bought by Amazon and are slowly integrating Kindle to it, so usually if you bought something digitally for Kindle it will also show up in Comixology. Unfortunately there is no cross buy, so if you buy physical you don't get digital. They also just recently started a subscription service, but only some things are included and it rotates.
Crunchyroll has a manga app which is probably the worst of them all. They simul publish a bunch of series, though, and you can read the most recent chapters for free, with ads, via the app. If you have a Crunchyroll premium subscription you can read the archives, though they don't have, for instance, the early chapters of Attack on Titan and Fairy Tail.