The ferry is not bad at all. We use the Crown Bay ferry, 5-6 mins from airport, and as long as you aren't running late have a drink or two at Tickles. We have done the Red Hook ferry but that was a PITA.
Yes Crown Bay - only minutes from airport. Only like $20 per person plus $5 per luggage. Very easy. Red Hook is about $75 cab ride just to get to the ferry.
We arrive at 2:40 PM. I'm assuming trying to make the 3:30 isn't possible after getting luggage etc. The last is at 5:30 so looks like we'll stop by Tickles.
I think that's doable as long as your luggage comes off conveyor in a reasonable amount of time. You go out the doors and tell the guys you want Crown Bay ferry. They'll pack you on busses and it's a real short drive. I'm jealous.