What kind of fuel should I use?
This is real easy: The owner's manual specifies 87 octane unleaded gasoline. Anything else is like throwing money out the window. If you thought the manual said to use 91 octane, you read it wrong.
Confusion comes about because the method of determining the octane number is different in North America than in most of the rest of the world. Other countries use the Research Octane Number (RON), but if you look at the yellow octane sticker on pumps in the US, you'll see a notation that (R+M)/2 is how octane is calculated. (R+M)/2 is an averaging of the RON and the Motor Octane Number (MON). The important bit to know is that 87 in the US is equal to 91 in countries using the RON standard.
You'll find that the same information is on page 29 of your owners manual:
Having too high an octane is never harmful, but having too low can be. That said, there's still no point in using an octane higher than what the factory says, unless the engine's knocking. With an older engine, sometimes you get knocking unless you go with a higher octane.
You're not going to get a performance gain with a higher octane fuel. Octane (which is the only difference between the cheap gas and the expensive gas at a station) is a detonation inhibitor. It does not make gasoline burn better in any way - it actually prevents the gas from burning too soon. This is very useful in a high-compression, high-performance engine, like those found in sports cars and high-performance motorcycles. That's why it's recommended for those engines. However, for the Ninja 250, having higher octane produces no benefit: detonation won't occur with 87 octane gas, and it will continue not to occur with 89 or 91 octane gas. It is literally blowing money out your tailpipe. Since higher octane only increases the ignition energy required to start the burning reaction, it may cause a very slight reduction in performance compared to lower octane gasoline, but it would be too small to be measured, much less noticed.
In other words, 87 octane and 91 octane gasoline perform exactly the same in a Ninja 250 engine. There is no benefit (but also no harm) to running 91 octane gasoline, and it costs 20 cents more per gallon, typically. Over the course of 10,000 miles at 60 mpg, you'll spend an extra $33 on nothing.
At higher elevations, usually in western mountain states, octane numbers will often be lower to compensate for different combustion conditions. You should be able to use the lowest-octane gas sold there in your Ninja 250, but if you experience anyor unusual noises from the engine, switch to a higher octane fuel or a different brand.