Thanks for the quick responses. I realize that it's not too late to get one. However, the problem is positioning myself to get into a top program.
My experiences post graduation, albeit three years, have been scattered because I wanted to explore options. I missed a couple of prime chances to continue into it (ie. after undergrad, after MS), so my mentors have known that it wasn't my original intent. In college, I wanted to do it only to go into academia or if I claim some great passion, while some of my classmates went into it with goals of entrepreneurship. The three years of exploring helped me personally, but the risks are greater.
The other inconsistency that prevented me from entering PhD earlier was that my interests span into the sciences, it's shown in my undergrad research, so some programs I find too traditional for my taste (I'm perhaps over thinking).
Finally, the practical component is that somehow I did well on the job, so I got into the MBA program, which is a more natural step (although I have gut reactions against it sometimes), and which may allow me to move on with life faster. If I pass up the opportunity, it will take me some years to build enough experience to get into a top program again. But if I go the MBA route, I cannot look back. Complicated?