We stayed at the Islander marina several years ago when it was new, and we have also stayed at the municipal dock next door. Wakes were not a problem at the marina, and are only a problem at the municipal dock if you are on the outside of the wall. Both locations are right next to the Antique Boat Museum (fabulous!) and an easy walk to the town center. Clayton is a very nice small river town, much nicer than Alexandria Bay, which is way too commercial for us. It also has a restored opera house which now has an interesting series of events during the season. I can readily recommend either the marina or the municipal dock, but you will need reservations until after Labor Day. I'm surprised they do not return your calls. Keep trying - they are worth it.
Keewaydin has safe slips and very good facilities, but it is a State Park and a long walk from Alexandria Bay, or anywhere else for that matter. I was there a month ago to have the Cosmic C pulled out for service (the only Honda dealer in the area is off the water!) and all slips were occupied.
There are several marinas in and around Alexandria Bay, and hotels like the Edgewood resort have big docks for guests, but for us A Bay is a place to visit, not stay.
Don't give up your trip. There are so many things to see in the Thousand Islands