By and far, the best Masters in Financial Engineering is at Berkeley Haas.
Certainly, Haas's program is very good.
However, I would say that similar programs at schools like Princeton and Chicago are quite comparable. True, they don't call them a "Master's of Financial Engineering". For example, Princeton's program is known as "Master in Finance", Chicago's is a "Master's of Science in Financial Mathematics". But it's just a name. It means nothing. At the end of the day, the goals of the programs are the the same: to train you for quantititative jobs in finance.
Hence, looked at that way, I don't know that I would say that Berkeley is "by and far" the best such program. They, as well as several others, are all very good programs.