What are you looking for by replacing your windows? How long do you want the windows to last? Do you want wood on the inside? Do you want to tilt the windows in order to clean them? Do you want windows that have average ratings or do you want windows that are rated really high? How long of a warranty do you need?
Generally new home builders like Andersen windows because the brand name sells the job.
Very few specialty window contractors use Andersen windows. Marvin has some very nice windows if you can afford the price tag. If you are looking for really good energy ratings then neither company comes close to the top of the list.
http://www.replacementwindowpros.com