Get a 3rd company to give you an estimate and go with whatever 2/3 say who have physically seen your setup and house.

Too big furnace won't let the furnace run long enough to get it's peak performance, too small a furnace will over work it.
Too big of air conditioner will cool but not run long enough to de humidify properly so it will cycle more. Too small of air conditioner will have to run longer to cool properly.

When we had our air conditioner replaced close to 20 years ago it was a smaller unit then the old one and we were worried a bit about it but we've never had any problems.