The iBooks app is better. But Amazon Kindle Store is cheaper and has a superior selection.
The books
Publishers are responsible for creating and making available the books in each store. Sometimes a book is exclusive to one store. In that case, you have no option of where you purchase it.
When a book is available in both stores, you must compare the price and quality on a book-by-book basis. This is easy to do because both stores offer free sample chapters. Books tend to be better formatted in the iBooks Store than in Kindle's Store. This can be critical for some genres, such as technical/programming books with graphics, code samples, and tables.
The ecosystem
iBookstore purchases can only be read on iPhone/iPod touch/iPad/Mac. Kindle purchases can also be read on Amazon's dedicated Kindle devices, Microsoft Windows, iOS, BlackBerry, Mac OS X, Android, webOS, Windows Phone, as well as in a web browser.
The apps
iBooks app:
- better interface (you even can turn off the skeuomorphic design features, if you prefer)
- it has less features, but the features it does have are better: dictionary, highlighting, type/fonts, footnotes, navigation, look and feel
- better PDF support
- iBookstore built-into-the-app for convenient browsing and purchasing
Kindle app:
- Sharing feature where you can publicly publish snippets from your book to kindle.amazon.com for linking-to in Twitter/Facebook. Example.
- Amazon creates an email address for you to send documents to your Kindle via email. E.g. yourname@kindle.com
- Con: You have to jump out to the web browser to browse and purchase content.
On an iPad, I prefer reading in iBooks because Apple executes the fundamentals better. Amazon's Kindle app has some nice differentiating features, though. All that said, at the end of the day, nothing's better than reading a basic novel on a standalone e-ink Kindle device.
Using iCloud doesn't necessarily means you'll have to use Mail on iCloud. You can still use your current mail provider to send/receive email on your iPad. Providing you can connect to your current provider using IMAP, Exchange or POP.
You can also create your iCloud account without having a @me.com address. I use my @gmail.com address as my Apple ID to connect to iCloud to sync Contacts, Calendars, etc.
Best Answer
Not directly to iBooks, no. But you can email it to whatever email account you have set up on the iPad. Then, using the Open With button you can send it to iBooks or any compatible app on your iPad.
I do this all the time with whitepapers I find on my work computer that I want to read on the train. Alternatively, I send my self a link to the file if it's not behind a paywall or lead generation form.