For Kindle and Kobo you can't buy books directly in them as they would be classified as in-app purchases, instead you need to go to their website, buy the books there, and then download them in their app - I don't know about Kobo, but the Kindle app has a Cloud button at the bottom of it which should all of your kindle books so that you can download them.
For iBooks, try closing it via the taskbar and see if the store works when you re-open the app : from the home screen (i.e. not with the iBooks app 'open' on-screen) double-click the home button to bring up the taskbar, then press and hold any of the apps on the taskbar for a couple of seconds or so until they start shaking, then press the '-' in the top left of the iBooks app to close it, and touch any part of the screen above the taskbar so as to stop the shaking and close the taskbar.
If that doesn't work also do a reset : press and hold both the sleep and home buttons for about 10 to 15 seconds (ignore the red slider), after which the Apple logo should appear - you won't lose any content, it's the iPad equivalent of a reboot.
You could try deleting the iBooks app and re-downloading it. First copy any content from it to your computer's iTunes via File > Transfer Purchases (File > Devices > Transfer Purchases if you have iTunes 11 on your computer) - whilst you should be able to re-download any ibooks purchases from the store (as long as they remain in the store), that should also copy and PDFs and/or epubs over, even though they aren't iTunes purchases, and you can then sync them back after re-downloading the app