As much as I'm biased towards Bay, I'd have to agree and say Lee is your guy. Bay has a lot of pop, but he strikes out a ton. Had he played the whole year, he would have competed for the team lead with "K"raig Wilson. If he hits .300 this year, I'd be happy.
Bay doesn't walk a whole lot either, thus decreasing his OBP. He does have good speed, but the Pirates rarely steal nor does he steal well.
It's hard to translate what Lee will do now that he's in the NL, but I'd still take what he's done in the past over what possible potential Bay has.
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blog (updated 6/21 - Pirates walkout.)