Walker Zimmerman is probably the best defensive prospect in the 2013 MLS draft. (The argument seems to be between him and Andrew Ferrell, who is more of a defender/midfield hybrid.) He's big, can score and has JaVale McGee levels of upside. (Let's just ignore how much of that upside McGee has actually delivered upon for the purposes of this.)
Past Zimmerman, there are still plenty of solid options that the Rapids could go for if Zimmerman is taken in the Top 5, which he likely will be. West Virginia's Eric Schoenle is one of them.
Schoenle has dropped down the draft boards a bit after a less-than-perfect senior year with the Mountaineers, but that was a bad year for the entire team, not just him. The biggest knock on him is his size -- though he is 6'2'', he is a slight 150 pounds, which might not be enough for a center back.
Even with the size concern, it shouldn't be too much of an ask for him to bulk up a bit for the MLS level, and he is a talented defender who was in the Generation Adidas discussion a season ago. It might be considered a 'reach' to grab him at No. 6, but it's the MLS Draft, where everything might as well be a reach.