I wouldn't recommend the unrelated MS. You would be much better off getting the ball rolling (i.e. via a paid or unpaid RA) in an area that you will be working in later on. There are some pros and some cons either way, but I don't think you will gain as much from the MS as you will be required to put into it. Imagine spending the time to do a thesis that doesn't really excite you (and then having to repeat the process for your PhD because they won't accept your unrelated thesis from your MS.)
Personally, I didn't get into any PhD programs the first year I applied, only Masters programs that did not offer any funding. I declined those offers (actually... I deferred one for a year, which is smart if it's an option), stuck around my undergrad school so I could keep doing research with my advisor, and studied a lot to retake the GREs. My scores went up, I had more research experience, and even stronger letters of recommendation after that extra year. When I reapplied the next year I had much better opportunities, and I ended up in a program that I am very, very happy with!
However, keep in mind that if you can't improve your application, an extra year isn't really going to help you.