Taken from this Lifehacker post:
Update: the part about Google Apps not having Reader is no longer correct so this method should work.
Migrating Google Reader
Here is a YouTube video or the following instructions.
Migrating your RSS feeds is probably the easiest part of this process, but it unfortunately only works with regular Google accounts (since Apps accounts do not have access to Reader). Just go into Google Reader's settings and click on the Import/Export tab. At the bottom, you'll see a link that says "Export Your Subscriptions as an OPML File" which will download a single file to your computer containing all of your feeds. Click on this link, and then go to the same Import/Export tab in Account 2's Settings. This time, click the Choose File button and navigate to the file you just downloaded. After uploading this file, all your feeds should show up in Reader. Note that this won't sync your read and unread counts, nor will it sync your starred or shared articles, so you'll have to re-star anything you still want to reference (and re-friend anyone you follow on Reader).