Since I'm in no rush to get one now and I don't even have money, I would like to start looking now in hopes a dealer will be willing to give me a good deal. Maybe a used ninja 250 will come in and they call me and offer me a good price. Or possibly a big discount on gear if I have to pay all their stupid fees, more than 20% which both bike stores offered so I guess it's a normal discount nothing amazing.
If you're nervous about doing the Craigslist thing, just know that sales guys love sure things. I'd go in and strike up a conversation with one sales guy, tell him your situation (working at Smashburger, getting ready to graduate, going to take the MSF). Tell him you're really looking for a good used Ninja 250, but you're a few months out from being able to get one. Get his card, touch base from time to time with him (phone, email, occasional drop by -- Maybe stop back in and get some of your gear there for the MSF).
Once the guy gets to know you, he'll take care of you when the time comes because he's got some emotional investment tied up in you (you're the eager, first time buyer, who isn't so sure about what to look out for, and he was like that once, too). When you're ready to buy and good Ninja 250 comes in, you'll be one of the first calls the guy makes.
But you just need to resign yourself to the fact that you're just not going to get a great deal on a used 250 at a dealership. Dealerships have overhead (rent, taxes, utilities, employee salaries, etc). Ninjas are a low margin, high volume product, and they are wildly popular with newer riders. Like someone said earlier, they have no reason to haggle because if you don't buy it the next guy will.
Personally, knowing your financial situation, I'd go the Craigslist route and save several hundo off the dealer price (the money you save could pay for the MSF and some gear).