It's likely that the major forces of the universe (death, nature/seasons, the heavens, etc.) in Naruto have god manifestations along the lines of Shinto (maybe some Buddhist elements mixed in there). I'm sure there are "other belief systems" (like the Jashin cult) which may or may not have concretely confirmable living gods.
The reason we don't hear about other gods is because, as Pain said, Konoha's "religion" is pretty much the Will of Fire/ancestor "worship." Shinigami was necessary for that jutsu (to look scary/cool). Otherwise, Naruto doesn't touch much on the subjects of gods, religions, unifying forces of the universe, why toast lands butter side down, etc.
The Fire Temple is interesting. It's a ninja temple, right? Or a temple associated with the ninja. There's a big statue in there...tengu, right? Anyone remember? Is it also dedicated to "the Will of Fire" or is there a god aspect there? (I'm sleepy so someone else can look it up.)
It should be noted that this is a world which has giant talking frogs.
I always thought these beings came from their own dimension (which would be interesting in terms of "where are all the gods?"), but now that I think about it, I don't remember that ever being stated. And Jiraiya trained on that mountain which *appears* to be a part of the human world.
So my question is where are all the giant animals hiding? In remote mountains or their own dimension (remember humans in the human world can be summoned too; ie. Iruka via scrolls from Chuunin Exam)?