We loved Cape Flattery Trail at Neah Bay!!!!!!!! My recommendation for a stay in the Neah Bay is the Elwha Dam RV Park it is a FANTASTIC park. It is only 72 miles from the Cape Flattery trail under 7 miles to the ferry to Victoria
and even more things to do in the area.. Enterprise car rental is close enough that they should be able to bring you a rental if you wanted to leave the RV at the park and explore in a car. If you do Elwha Dam RV Park offers a dog walking service where they will come to your RV while your gone and walk and feed your dogs.
At Glacier we stayed at the East Glacier KOA because they also have a dog walking service and this allowed us to take the all day Red Bus Tour of Glacier that picks up at the KOA.