Ferry would be first choice because it drops you off right near Wall St. But the train to Penn then Path to WTC is another option. Longer commute time but less expensive.

Depends on what part of Manhattan you're going to. My wife worked in FiDi and took the ferry. It was pretty reliable. Always on time. Packed some days but she was always able to get a seat. She said if she was working in midtown, the train would've been the better choice because Penn Station is right there. Commute times on paper look longer on the train, but it's all a matter of where you want to go. Keep in mind the ferry is way more expensive than the train, even with the multi-trip book. Oh, and the ferry does go to midtown, but again, it's all about where your final destination is and how much time and money you're willing to pay.