I completely agree with turnbolt that Donatello would win in a fight. I've trained extensively with all four of these weapons, Bo-staff the most, and I have to say that his weapon is the most well suited against the other three.
Here is the order I would put them in based off of their weapons:
Donatello- his weapon is both simple and versatile. It can withstand attacks from the sword, nunchuks, and sais.
Raphael- Sai's are a great defensive and offensive weapon. The prongs of the sai can be used to hook weapons, for instance Mikey's nunchuku or Leo's swords from the hilt. Also, with the sai against the outside of your arm, it is great for blocking weapons like the sword (this technique was originally used by ninjas who kept the sai's up their sleeve which led to samurai thinking they were made of steel).
Leonardo-The sword is a tricky one. While it is somewhat long range, I wouldn't say it's the best weapon of the bunch as it isn't great for disarming (unless you plan on chopping someones hand off

) and only good for swinging and blocking.
Mikey-His weapons are just too short range. Unlike Raph who has many ways to utilize the sai even though they are short range, Mikey is really just left with swinging the nunchuku in different ways.
In terms of who would win in the fight factoring in both their weapons and level of skill, I would still go with Donatello. He is a logistic thinker as well as a skilled fighter. I would knock Raph down to third tied with Mikey. Like I said, the sai is a great weapon if used with technique and finesse but Raph is a bit of a berserker. Leo is smart and a very skilled fighter but factoring in his weapon, I'm putting him in second overall.
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