I have to be honest, I find Jun Fukuda's Godzilla movies to be more entertaining than Ishiro Honda's. That's not a knock on Honda by any means, it's simply that Fukuda's films are more fun to watch, at least for me. That's why, when it comes to "Godzilla directors", there is Ishiro Honda and Jun Fukuda, and then there is everyone else. These two did it first, and they did it the best.
I think everyone here knows of my affinity towards Godzilla On Monster Island, however, when it comes to which of the five goji-flicks directed by Fukuda is his best, most, unique, the most enjoyable, etc. it becomes more difficult to decide, because all of them have something special going for them. I think that Godzilla Versus The Sea Monster and Son of Godzilla are not only the two best films that he did, I feel they are two of the best Godzilla movies, period. Personal sentiments aside, Godzilla On Monster Island is the most "un-Fukuda" of the bunch, as Tomoyuki Tanaka wanted him to craft a more "traditional" Godzilla movie, in the wake of the bizarre Godzilla vs. the Smog Monster. With all of the stock-footage, and the Ifukube stock-score, it plays more like a "Godzilla's Greatest Hits" on-the-cheap than anything Fukuda might have done. I still enjoy it more than any other Godzilla movie, with the exception of one.
Godzilla vs. Megalon and Godzilla vs. the Cosmic Monster, I feel, have the signature "look" of a Jun Fukuda film. Fast editing, anonymous thugs on motorcycles, secret agents, chase scenes, wildly colorful, weird music, etc. Cosmic Monster is clearly the most solid of the two, and while Megalon is clearly the cheapest-looking of all the Godzilla movies, Fukuda still manages to prove what a crafty veteran he was, because that movie could have easily been much worse.
So when it comes to Jun Fukuda's Godzilla movies, I break it down like this...
The Best - Godzilla Versus The Sea Monster and Son of Godzilla
Personal Favorite - Godzilla On Monster Island
...however, for the sake of this discussion, I choose Godzilla vs. the Cosmic Monster as Jun Fukuda's most solid and entertaining Godzilla movie, with Godzilla vs. Megalon getting and honorable mention.
"EVERYONE FORGET YOUR TROUBLES! ENJOY YOURSELVES!THERE'S NOTHING TO WORRY ABOUT!" - Gigantis The Fire Monster
"It was HUGE...It was...IT WAS LIKE A MONSTER!!! Suddenly the rocks rose...ALIVE!" - Godzilla 1985