Gorgo is honestly an underrated gem. Great effects and a heartfelt story.
Gamera beats them all, hands down. Daiei making the decision to bring him back with Shusuke Kaneko at the helm was a killer choice. From special effects, score, set design, suit design, casting and especially story, the Heisei trilogy considerably raised the bar for the kaiju genre (many people consider GIII to be the best kaiju film of all time, barely behind Godzilla 54). Godzilla films at the time were filmed over several months, to but put out in the December that year, and that plus budget restraints affected the quality, hard. GI and GIII took at least two years, and especially in the latter, it shows, big time. This gets a lot of angry reacts on facebook, but IMO, the Heisei Gamera trilogy is better than anything Godzilla did since 1964.
Its a shame Toho kind of screwed Kaneko when they hired him for GMK. He wanted two years to work on the film and wanted to use Anguirus and Varan, but Toho denied him that timeframe and wanted it out in a year, and made him change the monsters to Mothra and Ghidorah. He still churned out an amazing film, but just thinking about what might have been makes me sad.
Tough call. 54, 64, 74, 89, 91, 01, and 14 off the top of my head. I enjoy others but these are my big standout ones.