There isn't a single "best place" for booking a Disney resort stay. Sometimes you can find a great deal using an Orbitz discount code. And there are other times when booking through expedia.co.uk is a better deal. And then there are still other times when booking through an airline website can get you the resort you want when it's sold out on the Disney website. You just have to do your own research to find the best deal that suits your needs.
My preference for visiting Universal is to stay onsite at one of their resorts so that I can get FOTL access. I find that it's worth the cost of the room just for that perk alone, especially during busy periods. Paying for a Disney resort room and then shuttling back and forth for 2 or more days strikes me as a waste of precious vacation time and money. But there are people who do it because they hate to pack up and move their luggage once they have arrived at their resort destination.