ni has multiple meanings...literally it means two...but in thise sense it is short for 'ani' which means older brother. san is a typical suffix that means they are being polite. however in this sense it is very common for japanese to call their older brother ani-san because of social heirarchy/japanese culture and thusly it is not nessisarily polite, it is natural. the girl is probably calling you ni-san because she feels like you are a good friend and act as and older brother or male figure in her life. she shortens it to make it cuter and more friendly...
edit:
the kanji is different which is why this means brother. anywho, ani is not the same as onisan. onisan is someone else's older brother, ani or anisan is your older brother...wihch is why when she says ni-san she is being friendly. someone mentioned something about -chan. typically this is used to refer to younger females, females, or just friends. however when iwas in japan the guys didnt like to be called chan. young boys are refered to with the suffix kun, however men dont like this because it is childish but girls love it because they think it is cute. therefore some guys like it too. it is the same as 'boku' . the proper way to refer to yourself is watashi, but again, young boys use boku. girls think this is also cute so older boys use it too, sometimes. there are tons of ways to refer to yourself though...but whatever you do, do not refer to yourself in the third person. it sounds completely stupid in japanese and they dont think it is funny:
example: *me talking*
bad: Journer is a cool guy.
good english: I am a cool guy.
nihongo: journer-san wa sugoi hito desu yo.
the right way: watashi/boku wa sugoi hito desu yo.
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