This is hard, as I have both and can't imagine not owning both colors!
But you have to consider a few things if you can only have one or the other. The first thing is although it is a strong color, whiskey can actually be worn with a ton of clothing. I love wearing it with black, browns, white, patterned clothing, etc. The chocolate can be worn with a lot but doesn't "POP" with black and browns like the whiskey color does. So if you are a black/grey clothing person I'd go with whiskey.
However....Chloe makes THE BEST chocolate. Hands down. You will never see another designer come up with a chocolate as good as Chloe's. It's deep, rich and saturated indoors. Outdoors it's burgandy undertones make the bag look like ripe berries generously drizzled with chocolate syrup. Some bags make me describe them as food and Chloe's chocolate color is one of them!
So...in the end, it depends on your wardrobe. Because no matter how much you love a color if you don't wear it then it is a shame. What colors do you wear a lot?
Edit: Also, the texture of the bag makes a big difference to me. If you find a perfectly smooshy pebbly whiskey but can't find the same one for the chocolate then I would go whiskey. The only problem right now is whiskey is very very hard to find in the department stores and boutiques. I personally think that any whiskey out right now are from Spring '06. I don't think they were available for order for Fall '06. I think they are pushing that orange color (which, in my opinion is a bit strong).