Is Masters then PhD my best shot? (more info inside)

[socxer]

Hey all,

I am looking to eventually get into a PhD program at a top teir school for Neural Engineering (brain-computer interface or neural prostheses).

However, I pretty much acted like a major fuck-up during most of my undergrad career and I currently have (after 3 years) a 3.06 GPA at an Ivy with a good engineering reputation (Mech. Engineering major with certificates in robotics and bioengineering).

I also have the issue of disciplinary factors - I was forced to take a year off for violating the extremely strict alcohol policy. How screwed am I because of this? I am going to write this in my SoP as the turning point that made me finally get serious.

There are some redeeming factors though: outstanding GRE's - 800Q, 790V, 6.0AW

I'm also going to try as hard as I can next year to get a great senior thesis under my belt and some very solid LoR's.

So my question is, do I have any kind of shot at a top tier PhD program (I'm thinking JHU, Duke, etc)? Or would it be in my best interest to pursue a Masters at a decent school first, and dominate that, then apply for the top tier PhDs?

I'd really appreciate any responses or advice.