I wouldn't try to get speakers from the Apple store. You can probably get them for cheaper at other places. As for the best ones, it really depends on what you want; 2.1 or 5.1, how much money do you want to spend, what you plan to do with them, etc.
Bose Companion 5!!!! They're very expensive at $399 but they supposedly mimic 5.1 surround speakers with only 2 speakers and acoustimass module. I've had the Bose 3 for a while now and will be getting the Bose 5's soon...will let you know how they are!
The real question is how much you want to spend. If you like to listen to music in general, then it's worth investing in a decent system, which would include a dedicated stereo amplifier and speakers. But that's the more expensive end of things.
If you're talking small, portable speakers, I've personally never heard small speakers that sounded half decent. You're much better off with $200 headphones than with a $200 speaker system.
I've also never heard a Bose product that sounded good. Most audiophiles seem to agree that Bose is the biggest rip-off in home audio.