Couple of ideas...
Perhaps the Kenai Peninsula. There is plenty of water activities such as kayaking or river floating. Also lots of fishing if you include fishing as a water activity. They have all types of fishing such as drifting on the river (you ride a boat down the river), bank fishing, and offshore. There is also the Kenai Fjords National Park and Kenai National Wildlife Refuge you could go hiking in. The NP only has one place you can drive to, everything else is hike in or boat in. I went kayaking out of Seward and ended up meeting some really cool guys from Montana that I still keep in contact with. I ended up spending the rest of the time in Seward with them, walking back to my family's condo after running up a $250 bill at the restaurant for 5 of us for dinner, "Sorry I'm 8 hours late and oh look, my dinner is still on the table..." opps!
Evermor mentioned Denali. Great for hiking obviously. Buy a ticket on the green bus. I bought a hiking guide at the REI in Anchorage and used it to plan my hike. I hiked an area called Stony Dome. Just tell the bus driver when you want to get off and he will stop and let you off. When you want to get on a bus, just wave it down. Now most people on the bus are just on it for the ride. How can you possibly ride this bus and not get off? They also freak out when the bus stops and you get off. "You are going hiking? But we just saw a bear!" I know, that's why I am going! I could easily spend a month in Denali and not be ready to leave. Excellent if you are wanting to go hike. However, it might get pricey on the green bus as it is $20 a pop. I'm pretty sure that if you stay in the campground and get on the bus at that bus stop, you wouldn't have to have a ticket as they only checked tickets at the visitor center. I don't know if that is what they intended though. However, in Denali you aren't going to have as many options on the water activities. There are a couple rivers in the area for whitewater rafting or kayaking. There are guides you can go through in the area.
Final idea, any town on the inner passage. If I had like a few months with nothing to do in the summer, I would love to paddle the inner passage. Obviously plenty of water activities. For hiking, just about any place that isn't in the towns is part of the Tongass National Forest. You also have lots of whale watching. You can ride to state ferry to go between towns.
I went to Alaska last summer and while my trip is quite different from what you are planning, you may be interested in reading about it as I went kayaking and day hiking.
http://texags.com/main/forum.reply.asp?topic_id=1185062&forum_id=54 
