I generally avoid both, but if I had to pick one I'd go with Paddlefish. I think that Boathouse is the most overrated and overhyped restaurant on property. The food is mediocre at best, the service is adequate but nothing special (think Outback Steakhouse), and it's extremely overpriced.
Back when Paddlefish was Fulton's, I thought it was excellent for quite some time, but it too went downhill quickly in the later years of its existence. Paddlefish has brought some life back to the place, but I still don't see it as anything "special." I do, however, like their menu options better, and I think their seafood is slightly superior to Boathouse, so that's why I'd give it the win in this comparison.