Main problem with Bose is that they are a single driver design and have holes in the frequency range. James Earl Jones' " Darth Vader " voice sounds strange coming out of the Bose Acoustimass module instead of the cube speakers. I think ANY decent HTiB would sound better than Bose. I usually recommend the Onkyo HTiB in the $400 to $600 range because Onkyo uses real receivers in their HTiB. Yamaha might as well, but I prefer Audyssey room correction over YAPO.. Using standard components in HTiB just makes it easier to use the receiver part and upgrade the speakers later on.
The Audioengine A5+ are powered monitors and are generally used in PC-based, receiver-less setups. If your main goal is to have a clean setup with just a laptop or PC and some speakers, then I would go this route. I have a 11.2 main system but have a little 2.1 setup in the computer room for streaming Hulu Plus / Amazon Prime. I have the Emotiva Airmotiv 5 monitors plus SVS SB-1000 sub. The Airmotiv 5 are on sale now for $410. That is $10 more than the A5+ and you get a very accurate ribbon tweeter and double the RMS power over the A5+. Go with the A5+ if you like a "softer" sound though. Only thing I have left to do in the computer room is add a DC-1 DAC so I can pass DSD ( Sony high-resolution audio ) through USB to the speakers.
You could also put together your own speaker/receiver combo. I usually recommend Energy Take Classic 5.0 speakers and a mid-range Denon/Marantz/Onkyo 5.1 receiver ( refurb from Accessories4less ) along with a Polk PSW-505 sub ( or SVS SB/SP 1000 for higher budget. ) You should still be able to do this for under $1000 and have a system that would sink the Bose.