When you think about how money works, it's really pretty arbitrary. Money is just a token, a representation of something that everyone wants or needs. As was mentioned, instead of people actually trading water (something that was very valuable) in Fallout 1, the water merchants collected bottle caps and backed them with water. The caps represented water...that's why they had value. Again, money is worthless unless it represents something people want.
Precious metals have an intrinsic value (and are therefore perfect for use as currency) because they're pretty, rare, and have sought-after chemical properties. It's a pain for people to carry around precious metals, though, so people locked it up in vaults and minted/printed currency that represented the precious metals for convenience. Nowadays currency represents things that are a lot more abstract than that, but it stands that the make-up of the money itself doesn't really matter...the key is that someone is backing it with something that is actually worth something. It also helps if whatever is used as currency is difficult to counterfeit, obviously.
Unlike Fallout and Fallout 2, Fallout 3 gives no explanation as to why caps have value in the Capital Wasteland...I'd be interested to learn how they came to be used there.
Anyway, on-topic, I think all three choices are good ones. Given that it's many years after the war now, though, I'd say that caps are too easy to counterfeit. Poker chips might be more difficult...I mean, casinos get by without (apparently) too much trouble with counterfeiting. Since NCR was actively seeking control of precious metal resources for this purpose (keep in mind that there are other ways to get precious metals besides mining), I think that NCR coins would make a lot of sense as well. Heck, this long after the war I wouldn't be surprised to see NCR notes backed by the NCR treasury. So, I guess I vote poker chips (could be backed by the mob bosses in New Vegas) and coins made of precious metals...or even NCR notes I suppose.
It would also be cool for competing currencies to exist...so in NCR areas they don't take chips, and in New Vegas they get mad if you flash any of that "worthless" NCR currency around. It'd also be funny if they laughed at you for trying to pay with caps.
"We don't take them bottle caps, but if you got any lint er old toothpicks in yer pocket I got a bridge I'll sell ya haw haw haw...."