In most cases, water-based polyurethane will be your best choice, but this is not an absolute rule. We say this because water-based poly will give you the same results in less time. Also, oil-based finishes tend to be more expensive, as they are often made of organic oils processed from various plants. Obviously, water is always going to be cheaper than oil.
An oil-based finish is smoother, slicker, and shinier. For a floor surface, this is probably not the way to go. A surface like this will present an increased risk of slips and falls. If this area is trafficked by the public, it could even expose you to legal liabilities. Thus, I would generally recommend water-based polyurethane for a floor job.