I'd definitely go with 2 pumps, either 2 MP10s or an MP10 with an MP40. Placed on opposite sides of tank and set in anti-sync mode makes about the most random and chaotic flow, IMO. I ran 2 MP40s on my 36"x 24" 90 in that manner, probably at 50% or so power, and the tank was always rocking and rolling. I believe a 40G cube is probably about 21"x 21", so if you have them opposite each other MP10s would be plenty (again, IMO).
As for taking up space, you won't find a pump that takes up less space in the tank. The 40 is obviously bigger than the 10, but inside the tank neither takes up much space. The trade off is having the motors on the outside, of course, but I've never minded that.