Both have their pros and cons. Waterbased finishes dry faster, cure faster and have less fumes. And can be more durable than your typical OMU. However, don't lump them all together. Comparing HD products to what is available at the local flooring distributor is like comparing apples to oranges. Look for a local distributor that sells Bona finishes. TRAFFIC is considered by many to be the best. It's expensive however. If you want cheap from HD poly, here's the best one they carry, IMO. It's actually a fairly good oil-based poly. None of the waterbased finishes are very good.
http://www.minwax.com/products/protective/fast-poly.cfm