I think that both Sony and Yamaha are similar in their outlook regarding receivers/amps: Both companies refuse to use THX processing, both have very good "budget" (£450 or less) products and both have a very good collection of DSP modes. In terms of sound quality I think that they are similar, with budget amps at least, erring towards a brighter cinema sound. As you go up the cost ladder things change for Sony. I think that Sony get slightly less edgy and more relaxed, whereas Yamaha retain their in-yer-face attitude and generally sound a lot more powerful than similarly priced Sony products.
How an amp performs is subjective and your opinion will probably differ from mine on sound tonal issues. The bloke that was listening to my Sony 940 (which he bought) thought the sound was too warm and asked for the trebble tone to be turned up to max!
In general, and limited to the two brands mentioned the answer is clearly in favour of Yamaha.
But in the end it's all a matter of personal taste and there are other worthy contenders like e.g. Denon and Marantz.
That said the new Yammies are said to have a "warmer sound" ... whatever that actually means.