Try George Bach from Bach Heating & Air conditioning.
The office is in Mississauga but I believe he's a Milton resident.
He has other guys working for him also.
http://www.bbb.org/kitchener/business-r ... on-1136392
In our previous house we had the same issue with our Keeprite furnace.
The furnace was about 5 years old at the time and the fan starting making this really high pitched noise.
We had to replace the fan but upon further inspection the heat exchanger had multiple cracks which we were told is a very dangerous thing due to carbon monoxide issues. If you have a builder's model Keeprite it's a good thing to check out.
They are pretty busy but hopefully you'll be able to get George out to take a look.