Newport : Make sure to see Yaquina Head Natural Area. There is a classic lighthouse, open for tours, an interpretive center (although may be boring for a six-year-old), and beautiful tidepools perfect for exploring. You can pretty much always see seals in the area, and often whales.
Still in Newport, head for the Bayfront. The sea lions climb right up on the docks and you can see them up close. This makes a nice alternative to going into the Sea Lion Caves, although that is quite a unique experience.
The Newport Aquarium was just voted among the "Top 10 Best Aquariums for Kids", according to Parents Magazine. It is the only one in the Top 10 which is not in/near a major metropolitan area. You also may want to stop in to the Marine Science Center, located near the Aquarium. Operated by Oregon State University, it is free, and also has "touching tanks".
Even if you do not want to rent the equipment to try crabbing, it is fun to watch. Waldport has a small dock, also people crab off several dock areas along the Newport bayfront. Kids love watching the crabbing activity!
Cape Perpetua is beautiful, and if it is a clear day, take the 10 minute drive to the top, then stroll to the lookout hut. You can see for many miles.