There is no best company that makes replacement windows. All companies are known for what they specialize in and people choose them for that particular thing. If I were you I would research the companies and find the one that meets what you are looking for in a company that does replacement windows.
There are alot of varieties of replacment windows. It is important to shop around and get the best quality that fits your budget. Pella windows has been known to be fantastic. They are beautiful and are a quality product.
I got my windows replaced by a company called Clera windows & doors which is a Concord based company. They did a pretty good job. The windows and doors do not require any painting and do not let in much sound.