There's a very active group of guys who kayak on the North Shore. They're split 50/50 in both sit in vs sit on top yaks. I used a 12' sit in this summer and fall and will upgrade to a 14' sit on top this spring.
I think it will give me more flexibility in the estuaries and will make it easier to launch and land in the surf. The trade is that I may get a bit wetter launching in the surf and you store your equipment differently. The best bet is to try out a few models as demo's or see if you can find someone who will let you give their yak a paddle. Here's great link to a local yak site. I've met and fished with a bunch of these guys. Very friendly and very helpful.
http://www.newenglandkayakfishing.com/
It has some great articles on selecting and fitting out your yak.