I am seeing in google webmaster tool, they are suggesting me to set www or non-www for my new site.
which is better for SEO? or I should leave to google decide which is the best?
www vs. non www is irrelevant for SEO purposes on a new domain.
But, in order to avoid duplicate content issues on your site make sure you 301 redirect the one you don't choose to the one you do choose. For example, if you decide to go without the www then you should 301 redirect all the www to the non www using wildcards.
The reason you want to do that is because Google sees
www.thispage.com as a completely different page than thispage.com It will see those as two different web pages on two different domains. So Google can see those two pages as duplicate content if you don't do the 301 redirect. This is a common issue on ecommerce websites.
Wordpress automatically takes care of the redirect for you if your site is based on Wordpress.
If you have an older domain that has some juicy links pointing to it then you might want to choose the version of the domain that has the best links pointing to it. The reason you might want to do that is because there is a small amount of PageRank lost through a 301 redirect. So you might want to lose as little as possible. In 99.9% of situations that isn't going to be a factor though.