First thing to look at with a cycle with low miles that has been sitting is the gas and gas tank.
Did you completely drain the tank and look at the condition of the inside? Rust will plug up the screens and filters, so make sure the tank is in good condition and the gas is fresh. Use 87 without ethanol if it's available in your area.
Check the small fuel filter on the inside of the fuel line where it connects to the carb. You want it there, but it needs to be clean and in good condition.
The air filter needs to be clean and in good condition also. Be very careful not to over-oil a foam filter after cleaning.
Make sure the petcock is flowing fuel when a vacuum is applied, and not flowing when it's not.
Next is the carbs. Chances are they need a complete and thorough overhaul - not just some spraying with carb cleaner. That's where ducatiman comes in. It's worth investing some money in your Ninja due to the low miles if the rest of it is in good condition.
There's also an oil/filter change, coolant change, brake fluid change, chain adjustment and lube, and other maintenance items that need to be checked to make sure it's road worthy.
No matter how many miles are on them, or how good the tread is, tires need to be replaced after 5 years. Even though they may look good (chances are there are small cracks in the rubber), tires dry out and lose traction from age.
This page has a lot of Ninja-specific info that may help you -
https://faq.ninja250.org/wiki/Ninja250_Howto