Google Reader added an option to import the feeds from iGoogle, but you'll be able to use it only the first time you load the feed reader or by opening the welcome page. I assume that Google Reader wanted to help iGoogle users who need a more powerful feed reader.
The process of importing feeds is extremely painful, since Google Reader subscribes to each feed one by one. If you only have 5-10 feeds in iGoogle, it will import the feeds quickly, but you'll need to wait a lot longer if you have more than 50 subscriptions.
You can select the feeds that should be imported and Google Reader will convert iGoogle's tabs into folders.
Last year, I wrote a script that exports iGoogle feeds to OPML, so you can import them in other feed readers. It's more difficult to use than Google Reader's feature, but at least it's efficient.