Should look at contract prices
To estimate Apple's Flash cost, check the Digitimes article about contract prices:
http://www.digitimes.com/news/a20090909PR207.html
According to this article, I am pretty sure Apple is paying around $1 per GB of Flash, probably even lower - they must have committed to huge volumes over a number of years and of course negotiated a favorable price. So the Flash cost difference between 32 and 64GB would be in the $30 region (more likely even lower - remember, huge volume, negotiating power,...).
Since iPhone uses a single flash device, they need to stack 4 64Gb Flash dies into a single chip package to get 32GB.
I assume Apple is buying & committed to buy the largest flash dies available - 64Gb and beyond in the future.
This deal will push the Flash prices up in the short run, but long term capacity will increase & prices will go down, which is good, right?