I would like to get a 5 speaker surround sound system. I have a max of $900 to spend on it.

That's not going to be enough to do it "right", where by that I mean getting a Dolby Digital/DTS receiver with all the bells and whistles, and a bunch of good (i.e., non-Bose) speakers. At your price range, there's no way you're going to have 10" woofers or anything close. To do that sort of thing, you're looking at $1500-2500 for the pair of main speakers minimum.

My recommendation, given your tight budget, is to build your system in stages. Start off with a reasonable 5-channel receiver from your favorite Japanese vendor and add a pair of main speakers. This will probably come in under $1000. Then add in the surround speakers and a powered subwoofer later. In fact, some stores may give you (crappy) surround speakers for free. Your Bose "cube" speakers count as "crappy" for the purposes of our discussion.

Back when I was a grad student, my receiver was taken out by a lightning strike. I replaced it with a $450 Yamaha floor demo receiver, and they threw in a center, two rears, and all the necessary cabling. I quickly disabled the crappy center speaker, putting the amp into "phantom" mode, only using my two main speakers (quality Mission 2-way bookshelf speakers) and the two crappy rears. This worked fantastically.

I haven't priced out receivers lately, but I'll bet you can get Dolby Digital and DTS decoding somewhere in the $500-700 range. Toss in $350 or so for a reasonable pair of bookshelf speakers (go audition lots of them), and you've hit your budget.

One extreme example: a family friend has a pair of Klipschorns -- monstrous, huge, terribly impressive speakers. When he went to 5.1, he added a Klipsche center, some other subwoofer, and these tiny rear speakers from Boston Acoustics. I can't seem to find the model number right now, as Boston Acoustics web page seems to be down, but these things were barely larger than computer speakers. The trick is they're bidirectional (also called "dipole" speakers). They have cones firing in opposite directions. This helps diffuse the sound so you get less directionality / better ambience.

Myself, I've now got five speakers from VMPS Audio, a small California firm. My main speakers, RM2's, weigh 150 pound each and go happily down to 20Hz with their 12" woofer -- no real need for a subwoofer. My center and rear speakers are 626 Ribbon speakers. These have 8" woofers and ribbon midrange and tweeters. A pair of these would probably set you back something like $700-800, and would make for excellent main speakers in your apartment. You could drive them with a standard amp, but you're now breaking your budget by 50%. If you could afford it, though, that's what I'd recommend.