In my opinion, cold air FTW. Short ram reduces air restriction since it's shorter (duh), but absorbs the majority of the engine heat. Cold air intakes don't have to be
that close to the ground, it can/should feed off vents or opening from the front facial of the vehicle for cooler air.
Unless you run into a hose, and the hose rips through your filter, jams itself down the intake pipe and sprays a jet of water into your engine, THEN I would be worried

..but a lot of cold air intakes are slightly angled. Any water that gets through the filter would drip back out and maybe only a mist of water would make it through, but the intense heat from the combustion of the engine would just make it evaporate anyway.
That being said, I've giggled my way through puddles with my car and it was fine. I would choose the cold air intake for the simple fact that it brings in cooler air. A cooler engine is a happy engine