Pingel has lowering links for 88-02 Ninja 250 that will lower the rear of the bike about 2". Should be about right for you to get started on after taking the course on something like a Rebel 250. They are a bit pricey compared to the ones I recently bought for a 02 GS500, but since you already have the bike, they could be well worth the price.
http://www.pingelonline.com/lowering_links.htm
Tire changes are always worth considering but forget it for the Ninja 250, you won't find low profile tires to fit it's narrow wheels. Shaving the seat can be worthwhile though. Since you are 23 years old you won't be getting any taller, but at 73 I'm getting shorter.
The changes in handling and ride of the lowered bike will not be that significant to you as a new rider. The steering will be a bit slower but that could be a plus for a new rider and the ride will be a bit harsher but you can set the rear preload to the lightest setting Karate suggested above and it will be of little notice to you.
A friend of mine, a really big guy, recently bought a Hyabusa to add to a couple large cruisers he rides and lowered it's rear 4" for appearance reasons. I followed him thru some twisties for a couple hours and he wasn't dragging anything but his toes at a pace faster than you will probably be going for a little while at least.
He later was dragging the underbody a bit and found he would bottom the top of the tire against the inner fender with his wife aboard with him and settled for 2" lower. Your light weight will be a plus on a lowered bike, we both weigh more than twice as much as you.
and Good Luck!
there are only 2 kinds of bikes: It's a Ninja... look that one's a Harley... oh there's a Ninja... Harley...Ninja...
