Booth was feeling so awkward about the situation that he didn't know what to do. He wanted to get out of there and have some time to think, but he didn't want to be an asshat and leave Brennan alone with her new body. What was weird for him was hugely magnified for her.
No matter what, it was Brennan inside that masculine body. It was her telling him that he couldn't see the future. "How do you know? Maybe I took some lessons from Avalon!" He picked up the bottle of whiskey and took another swig, passing it to Brennan once more.
He nearly spewed his mouthful, though, when she countered with her own joke. It wasn't exactly funny, just amusing to hear her him attempt a joke considering the current state she was in.