I've got the Vitamix and the Ninja 900w professional and they are both great.
I use the Vitamix for smoothies, soups, dips etc but nothing too sticky (like peanut butter) because it's a bit fiddly to clean really stcky, gunky stuff off the blade. Despite what they say, just using the soapy water on a spin does not get all the peanut butter.
I use the Ninja for humous, nut butter, grinding coffee beans and small job like that. The design of the beaker means the blade is in the screw lid and exposed for easy cleaning. I can get my little glass brush right into the nooks.... easy easy.
So, I think the Vitamix makes THE best smoothies and soup but the Nutri Ninja wins on ease of cleaning and handling smaller quantities.