"Gamera" had a much higher percentage of what I would consider good quality films, however it's an unfair comparison seeing as it's 3 against 7. With that said, Kaneko continued to produce quality films after the "Gamera" trilogy, and without ever knowing what he could have produced if the series continued, well...
As I always say though, "quality" doesn't always amount to "entertainment" (and to be blunt, kaiju fans should understand this anyway).
A few years ago I would most likely have said "Godzilla", but to be honest "Gamera: Guardian of the Universe" has grown on me so much more over time, and I've always found "Gamera 3" a marvel in kaiju cinema. As I said earlier, it's akward trying to compare 7 films against 3, but then personally I find "Gamera: Guardian of the Universe" and "Gamera 3" to be far more entertaining the the Heisei series' best (in my opinion, "Godzilla" and "Godzilla vs. Biollante", although I have soft spots for "Godzilla vs. King Ghidorah" and "Godzilla vs. Destroyer" too).
If I were to rank them from best to worst, it would probably be something like this...
1) Gamera: Guardian of the Universe
2) Gamera 3: Revenge of Iris
3) Godzilla
4) Godzilla vs. Biollante
5) Gamera 2: Attack of Legion
6) Godzilla vs. King Ghidorah
7) Godzilla vs. Destroyer
Godzilla vs. Mechagodzilla
9) Godzilla vs. Mothra/Godzilla vs. Space Godzilla -
I don't particularly hate either of them, and really don't have a favourite either.