I was going to suggest www.shortinterest.com but apparently they have kicked the can. Too bad, they were a good resource.
It seems that it's only reported monthly: http://www.nasdaqtrader.com/asp/short_interest.asp Same with the NYSE: http://www.nyse.com/press/NT00072E4E.html
You can get the end of month short interest numbers for Nasdaq issues from Nasdaq or Viwes online but if you want NYSE short interest for a stock you'll have to download their montly PDF file and look it up manually (but note that the list is in alphabetical order by company name rather than by symbol). If you can convert PDF to text you could load it into a DB or spreadsheet if you want.