Can't really find anything on brand new bikes, but kbb.com and nada.com have guides on what 2003 models should be priced at as far as used.
All the bike mags will show is MSRP in all the buyers guide issues that you will see on the news stand.
here is a blurb I found on about.com:
By getting the amount that the dealer pays for the motorcycle, you know his "ready to sell price." This tells you his automatic profit margin percentage. This should come out to be 10% - 15%. The dealer will do his best to make 10% total profit on the motorcycle.
I looked at one site he suggested, but of course, they want you to PAY to find out what the invoice price is.
Are you looking for something from the big four?
aka Honda, Yamaha, Suzuki,Kawasaki?
If you're looking at Harleys, be ready to be raked over the coals/bent over on price.. there are a few that won't ream you, but most won't negotiate because they have waitng lists.
unless you want a V-Rod

Plus the jack up the price with their own "enhancements" that THEY like,(read most profit margin for them..) and will not sell the bike without them.
I saw a site that was like a rating on HD dealers, and it was like a stealer or dealer rating. can't remeber it tho' sorry.
You might try out of state dealerships as well, but you have to weigh the pros/cons on that as well. Sometimes the savings can be pretty good if you are willing to drive to another state to buy.
Check the smaller towns as well, smetimes they sell at a lower price than big city dealers because of lower overhead/rent costs, etc..
hope this helps a bit.