Command Blocks vs Bukkit Plugin, Performance?

This depends on how complex the system would be and what you want to do with it besides put it on the server. I'll leave you with a pro/con comparison between the two.

Command Block

Pros:

• Easier to create
• Anyone can use the map, not just you
• Don't have to be updated when major changes to the game are done

Cons:

• Redstone circuitry is laggy
• Circuitry can take up lots of space
• Still complex syntax, even though it is easier

Bukkit Plugin

Pros:

• Map is limited to the server, so it can't be stolen using a mod
• Less laggy
• Takes up no space

Cons:

• Can't distribute the map without it being limited to Bukkit servers
• Hard to code
• If you can't code, developers are expensive