I know exactly jack about publishing, but I'll throw my two cents in because I have done the electronic equivalent of cold calling from time to time.
I imagine most of the smaller online book retailers would constantly be looking for ways to distinguish them selves from Amazon and BarnesAndNoble.com. It seems to me that most people looking to buy Harry Potter would go to one of the big guys because of their reputation. I imagine the smaller guys have to focus on rare, old, or niche authors and books. I imagine a short, personal (but professional) email would at least be a worthwhile step. Once you get your affiliate program going, mention it in the email, it might encourage them to give your book some additional exposure.
Again, advice from someone in your industry would be more helpful. As a small-timer myself, I am constantly looking for ways to entice new clients, so I love when I receive a personal (not spam) from another small-timer who wants to try and work out a mutually beneficial arrangement. I guess the key is to convince them it isn't spam, maybe mention something unique about their site that you liked or ask them a question about one of their books.
Be creative. Maybe offer to host a banner for their site on your site. I needed an article writer to provide content for one of my sites. It sells Asian imports and feng shui items. Here again, I didn't know squat about feng shui, so writing the articles myself wasn't even an option. I started searching for feng shui consultants and professionals. I couldn't pay them, so the only incentive I could offer was advertisement on my site, further promotion as a feng shui authority, and a discount on my product line. I emailed about 7 professionals. They were all well respected in the feng shui community so I figured I would get a lot of egos and cold shoulders. Well I was right; I got a lot of both. But it turns out, my first choice for the position responded and accepted. Do a google search for "Janice Sugita" the first 3 pages of links are about interior design and feng shui related information; she's a rock star in the feng shui community.
This isn't quite like your situation, but I think there are some similarities that might give you some ideas.
Good Luck.
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