I just had this same problem. (macbook pro, OSX Lion) Here's what I did:
1) Use the Express Upload tool from within Snapfish.
2) Click "select photos and videos"
3) When the dialog box comes up that allows you to pick files, go to the gray sidebar on the left hand side of the window. Look under MEDIA (all the way on the bottom of the sidebar) and under that, click "Photos." DO NOT go to the sidebar and select "Pictures" from your Favorites. If you do this, your iPhoto library is grayed out and you cannot select it.
4) Click on the triangle next to iPhoto, click "Photos" and all your photos should appear below. Select as you would normally.
5) Click "open" (lower right corner) and your files should start importing into snapfish.