Webmaster and Analytics are meant for completely different things. I don't know that either one of them is "preferred", but could you clarify what you are trying to accomplish with these tools? "Preferred" for what exactly?
Using both, I use google webmaster tools to analyze keywords and knowing that which keywords I need to focus and ranking. Google analytics I use for to view traffic sources, I know these tools are relevant together so we need to use both for our websites.