They did this fight in a G-Force magazine a few years back during a monthly King of the Monsters tournament where readers would vote who would win. The battle was about even, but Godzilla got more votes than Gamera and won when Gamera was trying to summon his most powerful fireball, but Godzilla proved to be quicker and took him down with an atomic blast to the chest.

Outside of this, its hard to say. Gamera would have an advantage in the air and could possibly dodge Godzilla's atomic blasts. Godzilla could probably swat him Gamera away though with his tail.

I would also point out fanbase, but I'm not sure which monster is more popular now these days.