My Bacchus website (link in signature) has a cruising notes section with info on NY canals as well as some on the areas noted below.
Leaving Oswego Sackets Hbr is a pleasant stop on your way to 1,000 Is. Navy Point is a nice full service marina a short walk to town and some good restaurants.
Clayton NY is home of the Antique Boat Museum that is very well done.
Keewaydin is a State Park with campground, pool and marina. Short ride into Alex Bay ( day docks avail for small fee$) shops & restaurants but grocery is not walking distance. I understand the 1,000 Is Club marina is nice but haven't been there ( on an Island close to Alex Bay and Boldt Castle.
Docking recreational boats is not a problem at Boldt Castle.
Singer Castle is a little further east and an interesting stop w docking available.
For the trip from Alex Bay to Kingston the channel along the N / Canadian shore is protected and scenic
Kingston - Confederation Basin is a great stop near restaurants, shops, grocery, etc
Rideau - best to leave early AM to make the first (up) licker at Kingston Mills... its 4 locks (3 connected, turning basin + 1 addnl) and if you don't make the first lock it can be a couple hour wait.
Upper Brewers lock is a popular stop, with power available and it's the beginning of the scenic part of the Rideau.
If you like to anchor out Mortons Bay is accessible via a narrow marked cut off to the east... be careful with nav aid colors as they change going into this cut.
Jones Falls lock is another 4 lock series that is best to be there for first lock in AM. It gets busy so best to arrive early and wait on the blue line docks
This is the very scenic and enjoyable stretch with nice lakes connected w locks.
Davis lock is another popular one with power and good docks
Newborn lock a nice stop w power above and decent docking w/o power below. Sterling Lodge is a nice fishing camp w restaurant. & Barba short walk from the lock.
Westport has good docking and a good stop for provisioning and shopping. In town a short walk from the docks.
Beyond the Narrows lock on Big Rideau Lake has good anchorages near the Murphy Point Provincial Park as well as limited island docking (no power) & mooring cans near Col By Island
Smiths Falls has good docking and most everything in town. This is the start of basically the river run all the way to Ottawa. This is scenic and more developed but very different than the lower lakes section of the Rideau.