I rank Superman I over Superman II because even though both have stupid endings, the ending to Superman I is emotionally fulfilling. His emotions, the music swelling, and his hearing both his fathers in the clouds, giving him what to him are different advice, and then going up and traveling back--it satisfies on an emotional level. I actually like the movie more because of its nonsensical ending as opposed to in spite of it (Tangled).
Superman II, on the other hand, is unsatisfying and not fulfilling. It does not cap on a negative emotional scene with a positive one, but instead neutralizes it. I didn't even think of how stupid the Superman I ending was until later because I was so swept up in what was happening. I had to bite my lip not to shout "OH BULLSHIT" during the Superman II ending when I was in a theater at my college.
It should be known that originally Superman I was going to end with him sending both bombs into space, no time travel, and then Superman II was going to end with time travel; you can see this if you rent or buy the Donner Cut that Warner Brothers released a couple years ago.
Beyond the endings, I think they're both the best we've had of Superman movies, and I'd say that even against the Bruce Timm stuff. The first one treats the mythos was more majesty and respect than I would've ever expected from a comic to a film adaptation, especially in a time period where comics were much sillier than they are now. Superman II is a little sillier, though part of that is from studio meddling. Still, it treats the Clark-Lois relationship maturely up until the bar scene, and Zod is a stronger villain than Lex Luthor in these films (although Luthor is so much smarter in the first film). So I'd say they're both good movies for their own reasons, but I would rank the first one as a stronger film overall.