Newport has many great attractions that you might not want to miss. The historic bay front is uniquely interesting, a mix of tourist attractions and working waterfront. The Yaquina Head Outstanding Natural Area is on my top 10 list of places not to miss. It’s got a beautiful lighthouse, great views, bird watching, seal watching and beautiful tide pools if you visit at a low tide. The Oregon Coast Aquarium in Newport is a fantastic facility. Near Newport, Devil’s Punchbowl in Otter Rock is always worth a visit. There are also several great restaurants in Newport. If I chose between Nye Beach and Agate Beach, it would be Agate Beach. Both are pretty much just flat stretches of beach, but Agate Beach is closer to Yaquina Head and more scenic to me. In general, I prefer the beaches away from Newport and concentrate on the other attractions there.
That said, when it comes to where to stay, I do like Yachats because it is close to the amazing Cape Perpetua Scenic Area and Heceta Head. To the north is Seal Rock and you could make Newport area attractions a day trip from Yachats if you don’t check those off your list as you are headed down the Coast. Yachats is a small town with limited restaurants and shops. Florence is a fun town with good shops and restaurants, but keep in mind it is on the river and is not a beach destination.
Washburne State Park and Honeyman State Park (in the Oregon Dunes) are both great parks and campgrounds. Washburne puts you closer to beach attractions like those in and near the Cape Perpetua Scenic Area and Heceta Head. I love the hike from Washburne to the Heceta Head Lighthouse. The Hobbit Trail is shorter, leading to a sandy beach. Honeyman State Park has a nice nature trail, but beyond that you are trudging through dunes (not a bad thing, but not really a trail). Honeyman is surrounded by dune areas open to ATVs, so as you get further from the park’s core, the more you hear and see ATVs. Keep in mind, Honeyman also has a freshwater lake for swimming too. I hope this doesn’t make your choice harder, but for hiking the dunes, my choice would be the John Dellenback Dunes Trail near the Eel Creek Campground in Lakeside. You really get the feeling of the immensity of the dunes and ATV noise is as minimal as any other area I’ve found. A second choice for hiking would be setting off from the Oregon Dunes Day Use area south of Honeyman State Park. It makes an easy trek to the ocean, at least as easy as it can be walking through dunes.