Seriously conflicted about a graduate program option I graduated in 2013 with a degree in Botany from a state college on the west coast. Since then, I've worked for the Forest Service on a rare plants/ invasive weeds survey crew, and currently, work for the USDA as part of the Agricultural research service as a biological science technician. When I took the job, I was clear to my supervisor that I planned on attending graduate school after the two years I was committed to on the project. He was excited about this and very supportive of me. I went to work for on a number of projects involving plant physiology, plant biology, remote sensing etc. My goal with this position was
to take my academic record from my times as an undergraduate and supplement it with some applied experience, then to apply to graduate schools for the 2016/17 school year as a top tier candidate. I've worked hard to make sure my undergraduate grades, GREs, and letters of recommendation are of sufficient quality to single me out from a crowd of well qualified applicants. My thought was that this two years of experience would take me over the top, that this experience would take me from being a well qualified applicant to a top tier applicant/ the top applicant. I had been looking at applying to 3-4 top tier schools in plant genetics/ plant physiology (UC Davis, UC Berkeley, Cornell, Michigan State).

So fast forward a year and a half (this summer) and my boss approaches me with an offer. He wants to fund me to do a graduate program at the local land grant university. It would be a full assistantship and tuition waiver for the two years, which is an incredible offer. I wouldn't even have to apply to the school.

Here is my conflict: The offer is for a program I'm only tangentially interested in (weeds biology), from a department I don't really want to be involved with (crop science; but could make do), at a fairly low ranked state university. 

I also feel like I've set myself up for one good shot at getting into a highly competitive program, and that taking this offer will throw that away. I won't get the chance to use the letters of recommendation, undergraduate grades, GREs, that I worked hard for, only to go to a middling school to do a degree that I'm only kind-of interested in.

At the same time, it's a convincingly good offer, one that I would be incredibly unlikely to get again.

Note also, that the offer was made at a very strategic time. The offer would be for the 2015/16 school year (I wouldn't finish my 2 years under my original contract). He made the offer in such a way that it preempts my ability to apply to other schools and cultivate a counter offer.
I'd just state that the offer, while tempting, is second selection for you, and apply to the schools that interest you anyway. Worst case, you'll be rejected elsewhere. Don't close options unless you really have to.