Actually Pretty Popular!
Although I wouldn't list American football down as one of the most popular sports in Japan, it is popular to some extent. There is not real professional American football league. There are two leagues, the university league and the businessmen's league. The champion university team competes with the champion company team at the end of the year and this is called the Rice bowl. This is the biggest game of the year and is played at Tokyo Dome (home of the Tokyo Yomiuri Giants).
I have been to a couple of Obic seagulls games and they are pretty exciting. They also hold special exhibition matches from time to time such as Notre Dame OB v.s. the Japanese national team. That was also a great game. Going to a football game might be an interesting experience if you are a fan of football!
The reason why American football is fairly popular in Japan could be because there used to be a popular cartoon called "Eye Shield 21". This cartoon is based on a manga and so American football is something familiar to kinds from that generation.