I've done author portraits which were published on the back flap and received anywhere from $800 - $1400. One front cover portrait of Victoria Stillwell, $2000.
If they want your portrait for the front cover THEY WILL PAY. Your portrait is going to sell that book, so don't feel bad about asking for money. Any photographer deserves to get paid for their work, no matter their level of experience, "pro" vs "amateur" etc. Giving away your work will contribute to the decline of the photo industry.
What you need to be negotiating is rights for a single edition, so if the book goes into second, third editions you get paid again. They may also want editorial publication rights, which would make it okay for them to send the photo to a magazine to be published outside of the context of the book cover (that is, without the title, author name, etc.) Be careful there. That can be a big giveaway with a lot of potential -- and valuable -- uses.
You are in the driver's seat here. There is obviously ONE photograph that fits their needs and you own it. Being a scarce resource, you charge accordingly.
I would also register that image with the US Copyright Office as well, immediately.
If you need any help, just give me a shout.