I think paddle, absolutely. Theres nothing wrong with pedal kayaks, but theyre somewhat specialized. Fishers like them as they allow very quiet hands-free propulsion over shoals where fish may be waiting. Nature-watchers like them for the same reason.
Its true that pedal power yields a natural, fairly non-fatiguing way to propel a boat (your thigh muscles are the strongest ones on the body). But you lose some maneuverability. You lose some safety features (paddles are useful for a number of things, although you can always pack one along). And you lose that traditional feel" of kayaking.
Of course, which paddle kayak you get will depend a lot on budget. For your purposes, I think the Necky Manitou 13 ($829) would work great, as its a boat that combines some touring and recreational features. It has a nice, roomy cockpit and good stability. And its polyethylene hull is durable. If you decide some overnight trips are in your future, the larger Wilderness Systems Tsunami 175 ($1,500) offers more storage, an optional rudder, and a cockpit with lots of adjustments for more comfort. Its a nice boat, but, of course, youll be getting up there in price if you buy two.
How about a tandem? Another Wilderness Systems boat, the Pamlico 160T ($1,175), seats two and can even handle a little surf should you find some. It comes with a rudder and has easily adjusted seats.
I will say that pedaling has its appeal. Do you see pedal boats in the waters where you want to spend time? Maybe ask around, get some opinions. The Hobie Mirage Outfitter ($2,200) a tandem pedal boat, actually looks like it would be a lot of fun.
The Outside Buyer's Guide for Summer 2008 is on newsstands now. Look for it online soon.