The Yankee U makes a pretty compelling case that they did, at least to some degree. In one case, the Yankee U says the YES Network toolbar that appears above the River Avenue Blues website disappeared for a period of time after two of the site's writers expressed displeasure with the Soriano signing. In another case, the response may have been a bit more extreme.
Via the Yankee U, regarding a post titled "What the Heck Are the Yankees Doing?" on the Pinstriped Bible blog:
Pinstriped Bible is directly affiliated with the YES Network, as the site is designed to look like the YES homepage and is frequently featured on the YES front page. A few hours after being posted, Steve Goldman's post was suddenly pulled, only to reappear a number of hours later with a new title (Soriano Strengthens the Pen, But Do Dominoes Fall?) and a softened stance. A visit to the page shows the altered title and article, but the URL still contains the original title. I have the original article saved (available upon request), and the primary differences are a few sentences added in support of the deal, as well as the moving of a positive paragraph to the beginning of the article. When asked about the incident, Goldman declined to comment.
None of the bloggers involved offered a comment to the Yankee U, actually, and the site points out that, to the best of their knowledge, the network has not previously censored any of its affiliated blogs. Still, if it is indeed some form of censorship on the part of the Yankees or the YES Network, it revisits a discussion that's been going for years about what happens when a sports team is affiliated in some way with a reporter, broadcaster, or even an outlet that covers it. (Remember Marv Albert's departure from MSG in 2004, after a season in which he'd reportedly been told to be less critical of the Lenny Wilkens–era Knicks? This is not an entirely different discussion.)
In the meantime, if the Yankees really want to silence any criticism of the Soriano signing, they'll have to censor their own general manager.