I don't know about the Sony store charging top dollar, not anymore. While they can be more expensive some times, most books I've compared lately are either cheaper or within cents of other retailers.
IMO the best store currently for price and selection is Books On Board. Yes, they have reward dollars, but they make it quite clear what the price is without reward dollars. You can use the reward dollars that accumulate in your account at any time. You just don't get more reward dollars if you're using them to pay for something. What I do is don't factor in the rewards when shopping, there just an added bonus on certain purchases and when I've accumulated enough I use them all at once to get a 'free' book or at least a hefty discount.
For example...
(List) $6.99 - (Savings) $0.38 = (Price) $6.61
Rewards Dollars Earned: $0.17 through Jan 1st, 2035
Get this title for Net Cost: $6.44
What I do is just pay attention the the real price which is always in black.
Fictionwise's micropay is a little more complicated and when looking at prices straight up they're generally more expensive than BoB. If you decide to go to the trouble sometimes you can get a better deal in the long run I suppose by dealing with micropay.
As Kenny mentioned there's a list of stores in the Wiki...
https://wiki.mobileread.com/wiki/E-book_stores
...it's quite long, maybe too long?
Here are the stores I check when shopping for a book...
Amazon (doesn't do you any good without a Kindle)
Books On Board
Fictionwise
Shortcovers
Webscriptions (only sell Baen and a few other pubs, all DRM free)
Diesel Ebooks
The publisher's website (sometimes publishers, usually smaller pubs have the best deal)
Sometimes when I can't find what I want or the format I want I'll also check Ebooks About Everything and Ebooks.com just to be thorough.