Goal is to avoid high vehicle exhaust areas.
Northern Tier-ish -Late Spring/Early Summer
Fort Erie (I am thinking this is going to be the busiest area?)
Lake Erie Connector
As far as the Fort Erie part - there are three places you can cross the Niagara river - the bridges' names are Lewiston/Queenston Heights, Rainbow, and Peace, in order from north to south. I don't know what the ACA map suggested as I don't have one. However, I can tell you that you are best avoiding Niagara Falls NY and Buffalo. The route up the river on the Canadian side is quite picturesque, although quite winding. The only serious urbanization is the city of Niagara Falls, Ontario, and if you stick to the river you will go through the nice, as opposed to nasty, tourist section (a few blocks away from the river it is all touristy stores and traffic but right by the river it is parkland with one main road). If I had to choose a bridge to cross it would be the Rainbow bridge, but the trouble is Niagara Falls NY has been economically depressed for too many years and the roads are in very bad condition.
To really avoid exhaust you could take rural routes from Queenston Heights, and head well west of Niagara Falls, but then you'd miss the falls themselves, and they are really worth a look-see.
I live in Webster NY, which you will find a little west of Wolcott NY on your map. If you should choose to go off route as you pass through the general vicinity of Rochester, I can help with specifics.