You can confirm this by searching for 'hacker news' in Google; the #1 ranking URL is /newest, rather than the front page. This isn't term specific - the site doesn't appear for other terms that it usually ranks well for, such as "news.ycombinator.com" or "hn".
I've checked the usual technical reasons (html head canonical/robots meta tag, http headers, robots.txt issues) but I don't see anything untoward.
I'll keep looking into it, but I'm posting this here in case the admins/mods have made any changes recently that could have had an effect. There's a possibility that the URL has been removed by Google for some particular reason, though I can't think of many pages that deserve it less than HN.
I'll update this thread if I see anything, but hopefully someone else will post an answer before I figure it out....
Here's a link where I answered the same question about three weeks ago: https://news.ycombinator.com/item?id=5837004 , so this isn't a new issue. In fact, PG has been blocking various bots since 2011 or so; https://news.ycombinator.com/item?id=3277661 is one of the original discussions about this.
And to show this isn't a Google-specific issue, note that Bing's #1 result for the search [hacker news] is a completely different site, thehackernews.com: http://www.bing.com/search?q=hacker+news
In general, I think PG's priority is to have a useful, interesting site for hackers. That takes precedence and is the reason why I believe PG blocks most bots: so that crawling doesn't overload the site.