Ideally if there are only two choices you should ask it like this: Which one works better for you? But if there are more than two possible choices: What works best for you? Although in real life, people may ask "What works best..." when there are only two choices.

There are two issues worth discussing here: 1. whether to use "which" or "what" 2. whether to use "best" or "better" The two issues are independent of one another. Use "which" when there is a choice to be made. The number of possible choices is irrelevant. If there is no clear choice, use "what". For example, you should say "What is the best way to cook a lobster?" "Which" would not be wrong, but unless you mention various options it's better to say "what". Use "better" only if you have singled out one option for special consideration. The number of options does not matter. There can be 16 options or just 2 options. The only thing that matters is that one option merit special consideration. For example, suppose Mike has 15 tools that he can use to fix a car. You bring him a tool that you think is better than his. You say to him: "Mike, I think this tool is better than your 15 tools." To use "best", you would have to change 15 to 16: "Mike, take this tool. Of all these 16 tools, this one is the best."

either is fine